diff --git a/docs/module_structure.rst b/docs/module_structure.rst
index dc2e4b0..e22bf4e 100644
--- a/docs/module_structure.rst
+++ b/docs/module_structure.rst
@@ -320,7 +320,7 @@
   config("set_options_in_header_file") {
     cflags = [
       "-include",
-      rebase_path("my_config_overrides.h"),
+      rebase_path("my_config_overrides.h", root_build_dir),
     ]
   }
 
diff --git a/pw_arduino_build/arduino.gni b/pw_arduino_build/arduino.gni
index 0d1704c..f35836d 100644
--- a/pw_arduino_build/arduino.gni
+++ b/pw_arduino_build/arduino.gni
@@ -46,7 +46,8 @@
              _required_args_message)
 
   _arduino_selected_core_path =
-      rebase_path("$pw_arduino_build_CORE_PATH/$pw_arduino_build_CORE_NAME")
+      rebase_path("$pw_arduino_build_CORE_PATH/$pw_arduino_build_CORE_NAME",
+                  root_build_dir)
 
   arduino_builder_script =
       get_path_info("py/pw_arduino_build/__main__.py", "abspath")
@@ -60,7 +61,8 @@
              pw_arduino_build_PACKAGE_NAME + " list-boards")
 
   _compiler_path_override =
-      rebase_path(getenv("_PW_ACTUAL_ENVIRONMENT_ROOT") + "/cipd/pigweed/bin")
+      rebase_path(getenv("_PW_ACTUAL_ENVIRONMENT_ROOT") + "/cipd/pigweed/bin",
+                  root_build_dir)
 
   arduino_core_library_path = "$_arduino_selected_core_path/hardware/" +
                               "$pw_arduino_build_PACKAGE_NAME/libraries"
@@ -75,13 +77,13 @@
 
     # Save config files to "out/arduino_debug/gen/arduino_builder_config.json"
     "--config-file",
-    rebase_path(root_gen_dir) + "/arduino_builder_config.json",
+    rebase_path(root_gen_dir, root_build_dir) + "/arduino_builder_config.json",
     "--save-config",
   ]
 
   arduino_board_args = [
     "--build-path",
-    rebase_path(root_build_dir),
+    ".",
     "--board",
     pw_arduino_build_BOARD,
   ]
diff --git a/pw_bloat/bloat.gni b/pw_bloat/bloat.gni
index bb22417..6d79cfb 100644
--- a/pw_bloat/bloat.gni
+++ b/pw_bloat/bloat.gni
@@ -116,9 +116,10 @@
 
       # Allow each binary to override the global bloaty config.
       if (defined(binary.bloaty_config)) {
-        _bloaty_configs += [ rebase_path(binary.bloaty_config) ]
+        _bloaty_configs += [ rebase_path(binary.bloaty_config, root_build_dir) ]
       } else {
-        _bloaty_configs += [ rebase_path(pw_bloat_BLOATY_CONFIG) ]
+        _bloaty_configs +=
+            [ rebase_path(pw_bloat_BLOATY_CONFIG, root_build_dir) ]
       }
 
       _binary_path += ";" + "<TARGET_FILE($_binary_base)>"
@@ -131,7 +132,7 @@
       "--bloaty-config",
       string_join(";", _bloaty_configs),
       "--out-dir",
-      rebase_path(target_gen_dir),
+      rebase_path(target_gen_dir, root_build_dir),
       "--target",
       target_name,
       "--title",
@@ -165,7 +166,7 @@
         }
         script = "$dir_pw_bloat/py/pw_bloat/no_bloaty.py"
         python_deps = [ "$dir_pw_bloat/py" ]
-        args = [ rebase_path(_doc_rst_output) ]
+        args = [ rebase_path(_doc_rst_output, root_build_dir) ]
         outputs = [ _doc_rst_output ]
       }
 
@@ -250,7 +251,8 @@
     _linker_script_target_name = "${_prefix}_linker_script"
     config(_linker_script_target_name) {
       if (defined(_toolchain.linker_script)) {
-        ldflags = [ "-T" + rebase_path(_toolchain.linker_script) ]
+        ldflags =
+            [ "-T" + rebase_path(_toolchain.linker_script, root_build_dir) ]
         inputs = [ _toolchain.linker_script ]
       } else {
         ldflags = []
@@ -327,7 +329,7 @@
       }
       script = "$dir_pw_bloat/py/pw_bloat/no_toolchains.py"
       python_deps = [ "$dir_pw_bloat/py" ]
-      args = [ rebase_path(_doc_rst_output) ]
+      args = [ rebase_path(_doc_rst_output, root_build_dir) ]
       outputs = [ _doc_rst_output ]
     }
   }
diff --git a/pw_build/docs.rst b/pw_build/docs.rst
index db3725d..7bf075b 100644
--- a/pw_build/docs.rst
+++ b/pw_build/docs.rst
@@ -162,8 +162,6 @@
   specifying ``outputs``. If ``stamp`` is true, a generic output file is
   used. If ``stamp`` is a file path, that file is used as a stamp file. Like any
   output file, ``stamp`` must be in the build directory. Defaults to false.
-* ``directory``: Optional path. Change to this directory before executing the
-  command. Paths in arguments may need to be adjusted.
 * ``environment``: Optional list of strings. Environment variables to set,
   passed as NAME=VALUE strings.
 
@@ -208,7 +206,7 @@
 
   ``TARGET_FILE`` only resolves GN target labels to their outputs. To resolve
   paths generally, use the standard GN approach of applying the
-  ``rebase_path(path)`` function. With default arguments, ``rebase_path``
+  ``rebase_path(path, root_build_dir)`` function. This function
   converts the provided GN path or list of paths to be relative to the build
   directory, from which all build commands and scripts are executed.
 
@@ -266,7 +264,7 @@
     script = "py/postprocess_binary.py"
     args = [
       "--database",
-      rebase_path("my/database.csv"),
+      rebase_path("my/database.csv", root_build_dir),
       "--binary=<TARGET_FILE(//firmware/images:main)>",
     ]
     stamp = true
diff --git a/pw_build/error.gni b/pw_build/error.gni
index a7c0e69..653b4a9 100644
--- a/pw_build/error.gni
+++ b/pw_build/error.gni
@@ -41,9 +41,9 @@
       "--message",
       _message,
       "--root",
-      rebase_path("//"),
+      rebase_path("//", root_build_dir),
       "--out",
-      rebase_path(root_build_dir),
+      ".",
     ]
 
     # This output file is never created.
diff --git a/pw_build/exec.gni b/pw_build/exec.gni
index d2b4e69..fc6a5f9 100644
--- a/pw_build/exec.gni
+++ b/pw_build/exec.gni
@@ -72,14 +72,14 @@
   if (defined(invoker.env_file)) {
     _script_args += [
       "--env-file",
-      rebase_path(invoker.env_file),
+      rebase_path(invoker.env_file, root_build_dir),
     ]
   }
 
   if (defined(invoker.args_file)) {
     _script_args += [
       "--args-file",
-      rebase_path(invoker.args_file),
+      rebase_path(invoker.args_file, root_build_dir),
     ]
 
     if (defined(invoker.skip_empty_args) && invoker.skip_empty_args) {
diff --git a/pw_build/go.gni b/pw_build/go.gni
index 49230f2..eadb93b 100644
--- a/pw_build/go.gni
+++ b/pw_build/go.gni
@@ -149,7 +149,7 @@
     args = [
       "build",
       "-o",
-      rebase_path(target_out_dir),
+      rebase_path(target_out_dir, root_build_dir),
       invoker.package,
     ]
     deps = [
diff --git a/pw_build/host_tool.gni b/pw_build/host_tool.gni
index cac3f23..b5a1ffc 100644
--- a/pw_build/host_tool.gni
+++ b/pw_build/host_tool.gni
@@ -34,9 +34,9 @@
       "--src",
       "<TARGET_FILE(${invoker.tool})>",
       "--dst",
-      rebase_path("$root_out_dir/host_tools"),
+      rebase_path("$root_out_dir/host_tools", root_build_dir),
       "--out-root",
-      rebase_path(root_out_dir),
+      rebase_path(root_out_dir, root_build_dir),
     ]
 
     if (defined(invoker.name) && invoker.name != "") {
diff --git a/pw_build/linker_script.gni b/pw_build/linker_script.gni
index 7ba64ac..0cf681b 100644
--- a/pw_build/linker_script.gni
+++ b/pw_build/linker_script.gni
@@ -73,7 +73,7 @@
       # Treat the following file as a C file.
       "-x",
       "c",
-      rebase_path(invoker.linker_script),
+      rebase_path(invoker.linker_script, root_build_dir),
     ]
 
     # Include any explicitly listed c flags.
@@ -91,7 +91,7 @@
     # Set output file.
     args += [
       "-o",
-      rebase_path(_final_linker_script),
+      rebase_path(_final_linker_script, root_build_dir),
     ]
     outputs = [ _final_linker_script ]
   }
@@ -103,7 +103,7 @@
     if (!defined(invoker.ldflags)) {
       ldflags = []
     }
-    ldflags += [ "-T" + rebase_path(_final_linker_script) ]
+    ldflags += [ "-T" + rebase_path(_final_linker_script, root_build_dir) ]
   }
 
   # The target that adds the linker script config to this library and everything
diff --git a/pw_build/mirror_tree.gni b/pw_build/mirror_tree.gni
index 5e78de8..6091738 100644
--- a/pw_build/mirror_tree.gni
+++ b/pw_build/mirror_tree.gni
@@ -47,9 +47,9 @@
 
   _args = [
     "--source-root",
-    rebase_path(_root),
+    rebase_path(_root, root_build_dir),
     "--directory",
-    rebase_path(invoker.directory),
+    rebase_path(invoker.directory, root_build_dir),
   ]
 
   _deps = []
@@ -75,7 +75,8 @@
 
     _deps += [ ":$target_name._path_list" ]
     _args += [ "--path-file" ] +
-             rebase_path(get_target_outputs(":$target_name._path_list"))
+             rebase_path(get_target_outputs(":$target_name._path_list"),
+                         root_build_dir)
   }
 
   pw_python_action(target_name) {
@@ -85,7 +86,7 @@
     outputs = []
 
     if (defined(invoker.sources)) {
-      args += rebase_path(invoker.sources)
+      args += rebase_path(invoker.sources, root_build_dir)
 
       foreach(path, rebase_path(invoker.sources, _root)) {
         outputs += [ "${invoker.directory}/$path" ]
diff --git a/pw_build/py/pw_build/generate_python_package.py b/pw_build/py/pw_build/generate_python_package.py
index e70ce71..2ce4d62 100644
--- a/pw_build/py/pw_build/generate_python_package.py
+++ b/pw_build/py/pw_build/generate_python_package.py
@@ -105,7 +105,8 @@
 
     # Add all non-source files to package data.
     for file in (f for f in files if f.suffix != '.py'):
-        pkg = root / file.parent
+        pkg = file.parent
+
         package_name = pkg.relative_to(root).as_posix().replace('/', '.')
         pkg_data[package_name].add(file.name)
 
diff --git a/pw_build/py/pw_build/python_runner.py b/pw_build/py/pw_build/python_runner.py
index 15ce00e..5c38717 100755
--- a/pw_build/py/pw_build/python_runner.py
+++ b/pw_build/py/pw_build/python_runner.py
@@ -41,20 +41,17 @@
                         type=Path,
                         required=True,
                         help=('Path to the root of the GN tree; '
-                              'value of rebase_path("//")'))
+                              'value of rebase_path("//", root_build_dir)'))
     parser.add_argument('--current-path',
                         type=Path,
                         required=True,
-                        help='Value of rebase_path(".")')
+                        help='Value of rebase_path(".", root_build_dir)')
     parser.add_argument('--default-toolchain',
                         required=True,
                         help='Value of default_toolchain')
     parser.add_argument('--current-toolchain',
                         required=True,
                         help='Value of current_toolchain')
-    parser.add_argument('--directory',
-                        type=Path,
-                        help='Execute the command from this directory')
     parser.add_argument('--module', help='Run this module instead of a script')
     parser.add_argument('--env',
                         action='append',
@@ -164,7 +161,7 @@
 _MAIN_ARTIFACTS = '', '.elf', '.a', '.so', '.dylib', '.exe', '.lib', '.dll'
 
 
-def _get_artifact(build_dir: Path, entries: List[str]) -> _Artifact:
+def _get_artifact(entries: List[str]) -> _Artifact:
     """Attempts to resolve which artifact to use if there are multiple.
 
     Selects artifacts based on extension. This will not work if a toolchain
@@ -173,19 +170,19 @@
     assert entries, "There should be at least one entry here!"
 
     if len(entries) == 1:
-        return _Artifact(build_dir / entries[0], {})
+        return _Artifact(Path(entries[0]), {})
 
     filtered = [p for p in entries if Path(p).suffix in _MAIN_ARTIFACTS]
 
     if len(filtered) == 1:
-        return _Artifact(build_dir / filtered[0], {})
+        return _Artifact(Path(filtered[0]), {})
 
     raise ExpressionError(
         f'Expected 1, but found {len(filtered)} artifacts, after filtering for '
         f'extensions {", ".join(repr(e) for e in _MAIN_ARTIFACTS)}: {entries}')
 
 
-def _parse_build_artifacts(build_dir: Path, fd) -> Iterator[_Artifact]:
+def _parse_build_artifacts(fd) -> Iterator[_Artifact]:
     """Partially parses the build statements in a Ninja file."""
     lines = iter(fd)
 
@@ -212,7 +209,7 @@
         else:
             match = _GN_NINJA_BUILD_STATEMENT.match(line)
             if match:
-                artifact = _get_artifact(build_dir, match.group(1).split())
+                artifact = _get_artifact(match.group(1).split())
 
             line = next_line()
 
@@ -220,7 +217,7 @@
         yield artifact
 
 
-def _search_target_ninja(ninja_file: Path, paths: GnPaths,
+def _search_target_ninja(ninja_file: Path,
                          target: Label) -> Tuple[Optional[Path], List[Path]]:
     """Parses the main output file and object files from <target>.ninja."""
 
@@ -230,16 +227,16 @@
     _LOG.debug('Parsing target Ninja file %s for %s', ninja_file, target)
 
     with ninja_file.open() as fd:
-        for path, variables in _parse_build_artifacts(paths.build, fd):
+        for path, variables in _parse_build_artifacts(fd):
             # Older GN used .stamp files when there is no build artifact.
             if path.suffix == '.stamp':
                 continue
 
             if variables:
                 assert not artifact, f'Multiple artifacts for {target}!'
-                artifact = path
+                artifact = Path(path)
             else:
-                objects.append(path)
+                objects.append(Path(path))
 
     return artifact, objects
 
@@ -271,7 +268,7 @@
                 if line.startswith(statement):
                     output_files = line[len(statement):].strip().split()
                     if len(output_files) == 1:
-                        return paths.build / output_files[0]
+                        return Path(output_files[0])
 
                     break
 
@@ -283,7 +280,7 @@
         target: Label) -> Tuple[bool, Optional[Path], List[Path]]:
     ninja_file = target.out_dir / f'{target.name}.ninja'
     if ninja_file.exists():
-        return (True, *_search_target_ninja(ninja_file, paths, target))
+        return (True, *_search_target_ninja(ninja_file, target))
 
     ninja_file = paths.build / target.toolchain_name() / 'toolchain.ninja'
     if ninja_file.exists():
@@ -366,7 +363,7 @@
         if target.artifact is None:
             raise ExpressionError(f'Target {target} has no output file!')
 
-        if Path(target.artifact).exists():
+        if paths.build.joinpath(target.artifact).exists():
             yield _ArgAction.APPEND, str(target.artifact)
             return
 
@@ -441,7 +438,6 @@
 def main(
     gn_root: Path,
     current_path: Path,
-    directory: Optional[Path],
     original_cmd: List[str],
     default_toolchain: str,
     current_toolchain: str,
@@ -470,7 +466,7 @@
     if module is not None:
         command += ['-m', module]
 
-    run_args: dict = dict(cwd=directory)
+    run_args: dict = dict()
 
     if env is not None:
         environment = os.environ.copy()
diff --git a/pw_build/py/python_runner_test.py b/pw_build/py/python_runner_test.py
index 1ea69b0..f9e188c 100755
--- a/pw_build/py/python_runner_test.py
+++ b/pw_build/py/python_runner_test.py
@@ -194,6 +194,8 @@
         self._tempdir, self._outdir, self._paths = _create_ninja_files(
             NINJA_SOURCE_SET)
 
+        self._rel_outdir = self._outdir.relative_to(self._paths.build)
+
     def tearDown(self):
         self._tempdir.cleanup()
 
@@ -207,22 +209,22 @@
         self.assertTrue(target.generated)
         self.assertEqual(
             set(target.object_files), {
-                self._outdir / 'fake_source_set.file_a.cc.o',
-                self._outdir / 'fake_source_set.file_b.c.o',
+                self._rel_outdir / 'fake_source_set.file_a.cc.o',
+                self._rel_outdir / 'fake_source_set.file_b.c.o',
             })
 
     def test_executable_object_files(self):
         target = TargetInfo(self._paths, '//fake_module:fake_test')
         self.assertEqual(
             set(target.object_files), {
-                self._outdir / 'fake_test.fake_test.cc.o',
-                self._outdir / 'fake_test.fake_test_c.c.o',
+                self._rel_outdir / 'fake_test.fake_test.cc.o',
+                self._rel_outdir / 'fake_test.fake_test_c.c.o',
             })
 
     def test_executable_artifact(self):
         target = TargetInfo(self._paths, '//fake_module:fake_test')
         self.assertEqual(target.artifact,
-                         self._outdir / 'test' / 'fake_test.elf')
+                         self._rel_outdir / 'test' / 'fake_test.elf')
 
     def test_non_existent_target(self):
         target = TargetInfo(self._paths,
@@ -243,6 +245,8 @@
         self._tempdir, self._outdir, self._paths = _create_ninja_files(
             NINJA_SOURCE_SET_STAMP)
 
+        self._rel_outdir = self._outdir.relative_to(self._paths.build)
+
 
 class ExpandExpressionsTest(unittest.TestCase):
     """Tests expansion of expressions like <TARGET_FILE(//foo)>."""
@@ -260,7 +264,7 @@
             path.touch()
         else:
             assert not path.exists()
-        return str(path)
+        return str(path.relative_to(self._paths.build))
 
     def test_empty(self):
         self.assertEqual(list(expand_expressions(self._paths, '')), [''])
@@ -389,6 +393,8 @@
         self._tempdir, self._outdir, self._paths = _create_ninja_files(
             NINJA_SOURCE_SET_STAMP)
 
+        self._rel_outdir = self._outdir.relative_to(self._paths.build)
+
 
 if __name__ == '__main__':
     unittest.main()
diff --git a/pw_build/python.gni b/pw_build/python.gni
index b7bf71a..217a7f8 100644
--- a/pw_build/python.gni
+++ b/pw_build/python.gni
@@ -64,17 +64,17 @@
     ]
 
     if (defined(invoker.mypy_ini)) {
-      args += [ "--config-file=" + rebase_path(invoker.mypy_ini) ]
+      args +=
+          [ "--config-file=" + rebase_path(invoker.mypy_ini, root_build_dir) ]
       inputs = [ invoker.mypy_ini ]
     }
 
-    args += rebase_path(invoker.sources)
+    args += rebase_path(invoker.sources, root_build_dir)
 
     # Use this environment variable to force mypy to colorize output.
     # See https://github.com/python/mypy/issues/7771
     environment = [ "MYPY_FORCE_COLOR=1" ]
 
-    directory = invoker.directory
     stamp = true
 
     deps = invoker.deps
@@ -92,13 +92,13 @@
   pw_python_action_foreach(target_name) {
     module = "pylint"
     args = [
-      rebase_path(".") + "/{{source_target_relative}}",
+      rebase_path(".", root_build_dir) + "/{{source_target_relative}}",
       "--jobs=1",
       "--output-format=colorized",
     ]
 
     if (defined(invoker.pylintrc)) {
-      args += [ "--rcfile=" + rebase_path(invoker.pylintrc) ]
+      args += [ "--rcfile=" + rebase_path(invoker.pylintrc, root_build_dir) ]
       inputs = [ invoker.pylintrc ]
     }
 
@@ -108,7 +108,6 @@
     }
 
     sources = invoker.sources
-    directory = invoker.directory
 
     stamp = "$target_gen_dir/{{source_target_relative}}.pylint.passed"
 
@@ -151,10 +150,10 @@
 #       generate_setup is required in place of setup if proto_library is used.
 #   static_analysis: List of static analysis tools to run; "*" (default) runs
 #       all tools. The supported tools are "mypy" and "pylint".
-#   pylintrc: Optional path to a pylintrc configuration file to use. If not
-#       provided, Pylint's default rcfile search is used. Pylint is executed
-#       from the package's setup directory, so pylintrc files in that directory
-#       will take precedence over others.
+#   pylintrc: Path to a pylintrc configuration file to use. If not
+#       provided, Pylint's default rcfile search is used. As this may
+#       use the the local user's configuration file, it is highly
+#       recommended to pass this option to specify the rcfile explicitly.
 #   mypy_ini: Optional path to a mypy configuration file to use. If not
 #       provided, mypy's default configuration file search is used. mypy is
 #       executed from the package's setup directory, so mypy.ini files in that
@@ -346,10 +345,10 @@
                  "--label",
                  get_label_info(":$target_name", "label_no_toolchain"),
                  "--generated-root",
-                 rebase_path(_setup_dir),
+                 rebase_path(_setup_dir, root_build_dir),
                  "--setup-json",
-                 rebase_path("$_setup_dir/setup.json"),
-               ] + rebase_path(_sources)
+                 rebase_path("$_setup_dir/setup.json", root_build_dir),
+               ] + rebase_path(_sources, root_build_dir)
 
         # Pass in the .json information files for the imported proto libraries.
         foreach(proto, _import_protos) {
@@ -359,7 +358,7 @@
                   get_label_info(_label, "name") + ".json"
           args += [
             "--proto-library",
-            rebase_path(_file),
+            rebase_path(_file, root_build_dir),
           ]
         }
 
@@ -406,7 +405,7 @@
           args += [ "--editable" ]
         }
 
-        args += [ rebase_path(_setup_dir) ]
+        args += [ rebase_path(_setup_dir, root_build_dir) ]
 
         stamp = true
 
@@ -431,12 +430,13 @@
 
         module = "build"
 
-        args = [
-                 rebase_path(_setup_dir),
-                 "--wheel",
-                 "--no-isolation",
-                 "--outdir",
-               ] + rebase_path(metadata.pw_python_package_wheels)
+        args =
+            [
+              rebase_path(_setup_dir, root_build_dir),
+              "--wheel",
+              "--no-isolation",
+              "--outdir",
+            ] + rebase_path(metadata.pw_python_package_wheels, root_build_dir)
 
         deps = [ ":${invoker.target_name}" ]
         foreach(dep, _python_deps) {
@@ -509,12 +509,6 @@
         deps = _test_install_deps
         python_deps = _python_deps
 
-        if (defined(_setup_dir)) {
-          directory = rebase_path(_setup_dir)
-        } else {
-          directory = rebase_path(".")
-        }
-
         _optional_variables = [
           "mypy_ini",
           "pylintrc",
@@ -729,7 +723,7 @@
     foreach(_requirements_file, inputs) {
       args += [
         "--requirement",
-        rebase_path(_requirements_file),
+        rebase_path(_requirements_file, root_build_dir),
       ]
     }
 
diff --git a/pw_build/python_action.gni b/pw_build/python_action.gni
index fe31801..6ef48a4 100644
--- a/pw_build/python_action.gni
+++ b/pw_build/python_action.gni
@@ -32,10 +32,6 @@
 #                   creating their own placeholder file. If true, a generic file
 #                   is used. If false or not set, no file is touched.
 #
-#   directory       The directory from which to execute the Python script. Paths
-#                   in args may need to be adjusted to be relative to this
-#                   directory.
-#
 #   environment     Environment variables to set, passed as a list of NAME=VALUE
 #                   strings.
 #
@@ -60,23 +56,16 @@
     # GN root directory relative to the build directory (in which the runner
     # script is invoked).
     "--gn-root",
-    rebase_path("//"),
+    rebase_path("//", root_build_dir),
 
     # Current directory, used to resolve relative paths.
     "--current-path",
-    rebase_path("."),
+    rebase_path(".", root_build_dir),
 
     "--default-toolchain=$default_toolchain",
     "--current-toolchain=$current_toolchain",
   ]
 
-  if (defined(invoker.directory)) {
-    _script_args += [
-      "--directory",
-      rebase_path(invoker.directory),
-    ]
-  }
-
   if (defined(invoker.environment)) {
     foreach(variable, invoker.environment) {
       _script_args += [ "--env=$variable" ]
@@ -112,7 +101,7 @@
     _outputs += [ _stamp_file ]
     _script_args += [
       "--touch",
-      rebase_path(_stamp_file),
+      rebase_path(_stamp_file, root_build_dir),
     ]
   }
 
@@ -134,7 +123,7 @@
   _script_args += [ "--" ]
 
   if (defined(invoker.script)) {
-    _script_args += [ rebase_path(invoker.script) ]
+    _script_args += [ rebase_path(invoker.script, root_build_dir) ]
   }
 
   if (defined(invoker.args)) {
diff --git a/pw_build/python_dist.gni b/pw_build/python_dist.gni
index db41d1e..9514b94 100644
--- a/pw_build/python_dist.gni
+++ b/pw_build/python_dist.gni
@@ -58,11 +58,11 @@
 
     args = [
       "--prefix",
-      rebase_path(root_build_dir),
+      rebase_path(root_build_dir, root_build_dir),
       "--suffix",
-      rebase_path(_wheel_paths_path),
+      rebase_path(_wheel_paths_path, root_build_dir),
       "--out_dir",
-      rebase_path("${target_out_dir}/python_wheels"),
+      rebase_path("${target_out_dir}/python_wheels", root_build_dir),
     ]
 
     stamp = true
diff --git a/pw_build/zip.gni b/pw_build/zip.gni
index 653b0cd..60b3aa0 100644
--- a/pw_build/zip.gni
+++ b/pw_build/zip.gni
@@ -94,7 +94,7 @@
     script = "$dir_pw_build/py/pw_build/zip.py"
 
     args = [ "--out_filename" ]
-    args += [ rebase_path(invoker.output) ]
+    args += [ rebase_path(invoker.output, root_build_dir) ]
 
     inputs = []
     args += [ "--input_list" ]
@@ -107,8 +107,8 @@
 
         input_list = []
         input_list = string_split(input, _delimiter)
-        input_list[0] = rebase_path(input_list[0])
         inputs += [ input_list[0] ]
+        input_list[0] = rebase_path(input_list[0], root_build_dir)
 
         # Pass rebased and delimited path to script.
         args += [ string_join(_delimiter, input_list) ]
@@ -122,7 +122,7 @@
         dir = string_replace(dir, " $_delimiter", _delimiter)
         dir = string_replace(dir, "$_delimiter ", _delimiter)
 
-        args += [ rebase_path(dir) ]
+        args += [ rebase_path(dir, root_build_dir) ]
       }
     }
 
diff --git a/pw_docgen/docs.gni b/pw_docgen/docs.gni
index 50bf8d6..5759946 100644
--- a/pw_docgen/docs.gni
+++ b/pw_docgen/docs.gni
@@ -97,18 +97,19 @@
     "--gn-gen-root",
     rebase_path(root_gen_dir, root_build_dir) + "/",
     "--sphinx-build-dir",
-    rebase_path("$target_gen_dir/pw_docgen_tree"),
+    rebase_path("$target_gen_dir/pw_docgen_tree", root_build_dir),
     "--conf",
-    rebase_path(invoker.conf),
+    rebase_path(invoker.conf, root_build_dir),
     "--out-dir",
-    rebase_path(invoker.output_directory),
+    rebase_path(invoker.output_directory, root_build_dir),
     "--metadata",
   ]
 
   # Metadata JSON file path.
-  _script_args += rebase_path(get_target_outputs(":$_metadata_file_target"))
+  _script_args +=
+      rebase_path(get_target_outputs(":$_metadata_file_target"), root_build_dir)
 
-  _script_args += rebase_path(invoker.sources)
+  _script_args += rebase_path(invoker.sources, root_build_dir)
 
   if (pw_docgen_BUILD_DOCS) {
     pw_python_action(target_name) {
diff --git a/pw_hdlc/BUILD.gn b/pw_hdlc/BUILD.gn
index 41e5e4b..7ee98c1 100644
--- a/pw_hdlc/BUILD.gn
+++ b/pw_hdlc/BUILD.gn
@@ -125,7 +125,7 @@
 pw_python_action("generate_decoder_test") {
   outputs = [ "$target_gen_dir/generated_decoder_test.cc" ]
   script = "py/decode_test.py"
-  args = [ "--generate-cc-test" ] + rebase_path(outputs)
+  args = [ "--generate-cc-test" ] + rebase_path(outputs, root_build_dir)
   python_deps = [
     "$dir_pw_build/py",
     "py",
diff --git a/pw_polyfill/BUILD.gn b/pw_polyfill/BUILD.gn
index b173e06..6292b2d 100644
--- a/pw_polyfill/BUILD.gn
+++ b/pw_polyfill/BUILD.gn
@@ -40,7 +40,7 @@
     # without requiring a #include. This allows the use of newer C++ language
     # features in older C++ versions without an explicit include.
     "-include",
-    rebase_path("language_features.h"),
+    rebase_path("language_features.h", root_build_dir),
   ]
   visibility = [ ":*" ]
 }
diff --git a/pw_protobuf_compiler/proto.gni b/pw_protobuf_compiler/proto.gni
index 241c666..cc0cb27 100644
--- a/pw_protobuf_compiler/proto.gni
+++ b/pw_protobuf_compiler/proto.gni
@@ -49,7 +49,8 @@
     }
 
     _includes =
-        rebase_path(get_target_outputs(":${invoker.base_target}._includes"))
+        rebase_path(get_target_outputs(":${invoker.base_target}._includes"),
+                    root_build_dir)
 
     pw_python_action("$target_name._gen") {
       script =
@@ -79,15 +80,16 @@
                "--include-file",
                _includes[0],
                "--compile-dir",
-               rebase_path(invoker.compile_dir),
+               rebase_path(invoker.compile_dir, root_build_dir),
                "--out-dir",
-               rebase_path(_out_dir),
+               rebase_path(_out_dir, root_build_dir),
                "--sources",
-             ] + rebase_path(invoker.sources)
+             ] + rebase_path(invoker.sources, root_build_dir)
 
       if (defined(invoker.plugin)) {
         inputs = [ invoker.plugin ]
-        args += [ "--plugin-path=" + rebase_path(invoker.plugin) ]
+        args +=
+            [ "--plugin-path=" + rebase_path(invoker.plugin, root_build_dir) ]
       }
 
       if (defined(invoker.outputs)) {
@@ -104,8 +106,9 @@
     # Output a .json file with information about this proto library.
     _proto_info = {
       label = get_label_info(":${invoker.target_name}", "label_no_toolchain")
-      protoc_outputs = rebase_path(get_target_outputs(":$target_name._gen"))
-      root = rebase_path(_out_dir)
+      protoc_outputs =
+          rebase_path(get_target_outputs(":$target_name._gen"), root_build_dir)
+      root = rebase_path(_out_dir, root_build_dir)
       package = invoker.package
 
       nested_in_python_package = ""
@@ -118,7 +121,8 @@
       foreach(dep, invoker.deps) {
         dependencies +=
             rebase_path([ get_label_info(dep, "target_gen_dir") + "/" +
-                              get_label_info(dep, "name") + ".json" ])
+                              get_label_info(dep, "name") + ".json" ],
+                        root_build_dir)
       }
     }
     write_file("$target_gen_dir/$target_name.json", _proto_info, "json")
@@ -494,7 +498,7 @@
 
     # Indicate this library's base directory for its dependents.
     metadata = {
-      protoc_includes = [ rebase_path(_common.compile_dir) ]
+      protoc_includes = [ rebase_path(_common.compile_dir, root_build_dir) ]
     }
   }
 
diff --git a/pw_rpc/BUILD.gn b/pw_rpc/BUILD.gn
index 9f4a95f..bc82b77 100644
--- a/pw_rpc/BUILD.gn
+++ b/pw_rpc/BUILD.gn
@@ -232,7 +232,7 @@
   outputs = [ "$target_gen_dir/generated_ids_test.cc" ]
 
   script = "py/tests/ids_test.py"
-  args = [ "--generate-cc-test" ] + rebase_path(outputs)
+  args = [ "--generate-cc-test" ] + rebase_path(outputs, root_build_dir)
   python_deps = [
     "$dir_pw_build/py",
     "py",
diff --git a/pw_tokenizer/BUILD.gn b/pw_tokenizer/BUILD.gn
index 520beb2..2500f00 100644
--- a/pw_tokenizer/BUILD.gn
+++ b/pw_tokenizer/BUILD.gn
@@ -44,7 +44,7 @@
   if (current_os == "") {
     ldflags = [
       "-T",
-      rebase_path("pw_tokenizer_linker_sections.ld"),
+      rebase_path("pw_tokenizer_linker_sections.ld", root_build_dir),
     ]
   } else if (current_os == "linux" && !pw_toolchain_OSS_FUZZ_ENABLED) {
     # When building for Linux, the linker provides a default linker script.
@@ -53,10 +53,11 @@
     # default linker script instead of overriding it.
     ldflags = [
       "-T",
-      rebase_path("add_tokenizer_sections_to_default_script.ld"),
-      "-L",
-      rebase_path("."),
+      rebase_path("add_tokenizer_sections_to_default_script.ld",
+                  root_build_dir),
     ]
+    lib_dirs = [ "." ]
+
     inputs += [ "add_tokenizer_sections_to_default_script.ld" ]
   }
   visibility = [ ":*" ]
diff --git a/pw_tokenizer/database.gni b/pw_tokenizer/database.gni
index 81d6832..2508470 100644
--- a/pw_tokenizer/database.gni
+++ b/pw_tokenizer/database.gni
@@ -119,9 +119,9 @@
 
     args += [
       "--database",
-      rebase_path(_database),
+      rebase_path(_database, root_build_dir),
     ]
-    args += rebase_path(_input_databases)
+    args += rebase_path(_input_databases, root_build_dir)
 
     foreach(target, _targets) {
       args += [ "<TARGET_FILE($target)>$_domain" ]
@@ -134,9 +134,8 @@
     }
 
     if (defined(invoker.optional_paths)) {
-      _paths = rebase_path(invoker.optional_paths)
-      _out_dir = rebase_path(root_build_dir)
-      assert(filter_include(_paths, [ "$_out_dir/*" ]) == _paths,
+      _paths = rebase_path(invoker.optional_paths, root_build_dir)
+      assert(filter_include(_paths, [ "../*" ]) == [],
              "Paths in 'optional_paths' must be in the out directory. Use " +
                  "'input_databases' for files in the source tree.")
       args += _paths
diff --git a/pw_toolchain/arm_clang/clang_config.gni b/pw_toolchain/arm_clang/clang_config.gni
index 2c71a2f..de212b9 100644
--- a/pw_toolchain/arm_clang/clang_config.gni
+++ b/pw_toolchain/arm_clang/clang_config.gni
@@ -12,7 +12,8 @@
 # License for the specific language governing permissions and limitations under
 # the License.
 
-_script_path = rebase_path("../py/pw_toolchain/clang_arm_toolchain.py")
+_script_path =
+    get_path_info("../py/pw_toolchain/clang_arm_toolchain.py", "abspath")
 
 # This template generates a config that can be used to target ARM cores using
 # a clang compiler.
diff --git a/pw_toolchain/default/BUILD.gn b/pw_toolchain/default/BUILD.gn
index e961c97..e8ad524 100644
--- a/pw_toolchain/default/BUILD.gn
+++ b/pw_toolchain/default/BUILD.gn
@@ -24,5 +24,6 @@
   # If the user tries to build a target with the default toolchain, run a script
   # printing out the error.
   command = "python " +
-            rebase_path("$dir_pw_toolchain/py/pw_toolchain/bad_toolchain.py")
+            rebase_path("$dir_pw_toolchain/py/pw_toolchain/bad_toolchain.py",
+                        root_build_dir)
 }
diff --git a/pw_toolchain/non_c_toolchain.gni b/pw_toolchain/non_c_toolchain.gni
index 04e7013..53f7bdd 100644
--- a/pw_toolchain/non_c_toolchain.gni
+++ b/pw_toolchain/non_c_toolchain.gni
@@ -41,14 +41,15 @@
   _command = string_join(" ",
                          [
                            "python",
-                           rebase_path("$dir_pw_build/py/pw_build/error.py"),
+                           rebase_path("$dir_pw_build/py/pw_build/error.py",
+                                       root_build_dir),
                            "--message \"$_message\"",
                            "--target",
                            _label,
                            "--root",
-                           rebase_path("//"),
+                           rebase_path("//", root_build_dir),
                            "--out",
-                           rebase_path(root_build_dir),
+                           ".",
                          ])
 
   if (defined(invoker.command)) {
diff --git a/pw_toolchain/py/pw_toolchain/clang_arm_toolchain.py b/pw_toolchain/py/pw_toolchain/clang_arm_toolchain.py
index 7494727..5c0cf61 100644
--- a/pw_toolchain/py/pw_toolchain/clang_arm_toolchain.py
+++ b/pw_toolchain/py/pw_toolchain/clang_arm_toolchain.py
@@ -32,6 +32,7 @@
 
 import argparse
 import sys
+import os
 import subprocess
 
 from pathlib import Path
@@ -88,8 +89,10 @@
 
 def get_compiler_info(cflags: List[str]) -> Dict[str, str]:
     compiler_info: Dict[str, str] = {}
-    compiler_info['gcc_libs_dir'] = str(get_gcc_lib_dir(cflags))
-    compiler_info['sysroot'] = _compiler_info_command('-print-sysroot', cflags)
+    compiler_info['gcc_libs_dir'] = os.path.relpath(
+        str(get_gcc_lib_dir(cflags)), ".")
+    compiler_info['sysroot'] = os.path.relpath(
+        _compiler_info_command('-print-sysroot', cflags), ".")
     compiler_info['version'] = _compiler_info_command('-dumpversion', cflags)
     compiler_info['multi_dir'] = _compiler_info_command(
         '-print-multi-directory', cflags)
diff --git a/pw_toolchain/universal_tools.gni b/pw_toolchain/universal_tools.gni
index 820276d..eafc0e8 100644
--- a/pw_toolchain/universal_tools.gni
+++ b/pw_toolchain/universal_tools.gni
@@ -19,8 +19,8 @@
     cp_command = "cp -af {{source}} {{output}}"
 
     # Use python script in absence of cp command.
-    copy_tool_path =
-        rebase_path(dir_pw_toolchain) + "/py/pw_toolchain/copy_with_metadata.py"
+    copy_tool_path = rebase_path(dir_pw_toolchain, root_build_dir) +
+                     "/py/pw_toolchain/copy_with_metadata.py"
     fallback_command = "python $copy_tool_path {{source}} {{output}}"
 
     command = "cmd /c \"($cp_command > NUL 2>&1) || ($fallback_command)\""
diff --git a/pw_unit_test/py/pw_unit_test/test_runner.py b/pw_unit_test/py/pw_unit_test/test_runner.py
index 0d395ae..52e69b6 100644
--- a/pw_unit_test/py/pw_unit_test/test_runner.py
+++ b/pw_unit_test/py/pw_unit_test/test_runner.py
@@ -23,6 +23,7 @@
 import subprocess
 import sys
 
+from pathlib import Path
 from typing import Dict, Iterable, List, Optional, Sequence, Set, Tuple
 
 import pw_cli.log
@@ -136,7 +137,13 @@
             test_counter = f'Test {idx:{len(total)}}/{total}'
 
             _LOG.info('%s: [ RUN] %s', test_counter, test.name)
-            command = [self._executable, test.file_path, *self._args]
+
+            # Convert POSIX to native directory seperators as GN produces '/'
+            # but the Windows test runner needs '\\'.
+            command = [
+                str(Path(self._executable)),
+                str(Path(test.file_path)), *self._args
+            ]
 
             if self._executable.endswith('.py'):
                 command.insert(0, sys.executable)
diff --git a/pw_unit_test/test.gni b/pw_unit_test/test.gni
index 02d9e26..fc112cf 100644
--- a/pw_unit_test/test.gni
+++ b/pw_unit_test/test.gni
@@ -185,7 +185,7 @@
       python_deps = [ "$dir_pw_cli/py" ]
       args = [
         "--runner",
-        rebase_path(pw_unit_test_AUTOMATIC_RUNNER),
+        rebase_path(pw_unit_test_AUTOMATIC_RUNNER, root_build_dir),
         "--test",
         "<TARGET_FILE(:$_test_to_run)>",
       ]
diff --git a/targets/arduino/BUILD.gn b/targets/arduino/BUILD.gn
index 7217dff..0032273 100644
--- a/targets/arduino/BUILD.gn
+++ b/targets/arduino/BUILD.gn
@@ -32,7 +32,7 @@
   if (current_toolchain != default_toolchain) {
     config("arduino_build") {
       # Debug: Print out arduinobuilder.py args
-      # print(string_join(" ", [rebase_path(arduino_builder_script)] + arduino_show_command_args))
+      # print(string_join(" ", [rebase_path(arduino_builder_script, root_build_dir)] + arduino_show_command_args))
 
       # Run prebuilds
       # TODO(tonymd) This only needs to be run once but it's happening multiple times.
diff --git a/targets/arduino/target_docs.rst b/targets/arduino/target_docs.rst
index a6f6b0b..379da1b 100644
--- a/targets/arduino/target_docs.rst
+++ b/targets/arduino/target_docs.rst
@@ -217,7 +217,7 @@
 
   _library_args = [
     "--library-path",
-    rebase_path(arduino_core_library_path),
+    rebase_path(arduino_core_library_path, root_build_dir),
     "--library-names",
     "Time",
     "Wire",
diff --git a/third_party/nanopb/BUILD.gn b/third_party/nanopb/BUILD.gn
index 35620ac..c718d9f 100644
--- a/third_party/nanopb/BUILD.gn
+++ b/third_party/nanopb/BUILD.gn
@@ -54,7 +54,7 @@
     sources = [ "generate_nanopb_proto.py" ]
     pylintrc = "$dir_pigweed/.pylintrc"
     action = {
-      args = [ rebase_path(dir_pw_third_party_nanopb) ]
+      args = [ rebase_path(dir_pw_third_party_nanopb, root_build_dir) ]
       stamp = true
     }
   }