diff --git a/pw_protobuf/BUILD.gn b/pw_protobuf/BUILD.gn
index ebe8636..562850f 100644
--- a/pw_protobuf/BUILD.gn
+++ b/pw_protobuf/BUILD.gn
@@ -95,12 +95,12 @@
 
 pw_proto_library("codegen_test_protos") {
   sources = [
-    "pw_protobuf_protos/test_protos/full_test.proto",
-    "pw_protobuf_protos/test_protos/imported.proto",
-    "pw_protobuf_protos/test_protos/importer.proto",
-    "pw_protobuf_protos/test_protos/non_pw_package.proto",
-    "pw_protobuf_protos/test_protos/proto2.proto",
-    "pw_protobuf_protos/test_protos/repeated.proto",
+    "pw_protobuf_test_protos/full_test.proto",
+    "pw_protobuf_test_protos/imported.proto",
+    "pw_protobuf_test_protos/importer.proto",
+    "pw_protobuf_test_protos/non_pw_package.proto",
+    "pw_protobuf_test_protos/proto2.proto",
+    "pw_protobuf_test_protos/repeated.proto",
   ]
   deps = [ ":common_protos" ]
 }
diff --git a/pw_protobuf/CMakeLists.txt b/pw_protobuf/CMakeLists.txt
index 66fc333..44ed7dc 100644
--- a/pw_protobuf/CMakeLists.txt
+++ b/pw_protobuf/CMakeLists.txt
@@ -27,10 +27,10 @@
 
 pw_proto_library(pw_protobuf.codegen_test_protos
   SOURCES
-    pw_protobuf_protos/test_protos/full_test.proto
-    pw_protobuf_protos/test_protos/imported.proto
-    pw_protobuf_protos/test_protos/importer.proto
-    pw_protobuf_protos/test_protos/non_pw_package.proto
-    pw_protobuf_protos/test_protos/proto2.proto
-    pw_protobuf_protos/test_protos/repeated.proto
+    pw_protobuf_test_protos/full_test.proto
+    pw_protobuf_test_protos/imported.proto
+    pw_protobuf_test_protos/importer.proto
+    pw_protobuf_test_protos/non_pw_package.proto
+    pw_protobuf_test_protos/proto2.proto
+    pw_protobuf_test_protos/repeated.proto
 )
diff --git a/pw_protobuf/codegen_test.cc b/pw_protobuf/codegen_test.cc
index 385de2f..faceb51 100644
--- a/pw_protobuf/codegen_test.cc
+++ b/pw_protobuf/codegen_test.cc
@@ -23,11 +23,11 @@
 // The purpose of the tests in this file is primarily to verify that the
 // generated C++ interface is valid rather than the correctness of the
 // low-level encoder.
-#include "pw_protobuf_protos/test_protos/full_test.pwpb.h"
-#include "pw_protobuf_protos/test_protos/importer.pwpb.h"
-#include "pw_protobuf_protos/test_protos/non_pw_package.pwpb.h"
-#include "pw_protobuf_protos/test_protos/proto2.pwpb.h"
-#include "pw_protobuf_protos/test_protos/repeated.pwpb.h"
+#include "pw_protobuf_test_protos/full_test.pwpb.h"
+#include "pw_protobuf_test_protos/importer.pwpb.h"
+#include "pw_protobuf_test_protos/non_pw_package.pwpb.h"
+#include "pw_protobuf_test_protos/proto2.pwpb.h"
+#include "pw_protobuf_test_protos/repeated.pwpb.h"
 
 namespace pw::protobuf {
 namespace {
diff --git a/pw_protobuf/pw_protobuf_protos/test_protos/full_test.proto b/pw_protobuf/pw_protobuf_test_protos/full_test.proto
similarity index 100%
rename from pw_protobuf/pw_protobuf_protos/test_protos/full_test.proto
rename to pw_protobuf/pw_protobuf_test_protos/full_test.proto
diff --git a/pw_protobuf/pw_protobuf_protos/test_protos/imported.proto b/pw_protobuf/pw_protobuf_test_protos/imported.proto
similarity index 100%
rename from pw_protobuf/pw_protobuf_protos/test_protos/imported.proto
rename to pw_protobuf/pw_protobuf_test_protos/imported.proto
diff --git a/pw_protobuf/pw_protobuf_protos/test_protos/importer.proto b/pw_protobuf/pw_protobuf_test_protos/importer.proto
similarity index 93%
rename from pw_protobuf/pw_protobuf_protos/test_protos/importer.proto
rename to pw_protobuf/pw_protobuf_test_protos/importer.proto
index 3f0e43b..39ad8b9 100644
--- a/pw_protobuf/pw_protobuf_protos/test_protos/importer.proto
+++ b/pw_protobuf/pw_protobuf_test_protos/importer.proto
@@ -13,7 +13,7 @@
 // the License.
 syntax = "proto3";
 
-import 'pw_protobuf_protos/test_protos/imported.proto';
+import 'pw_protobuf_test_protos/imported.proto';
 import 'pw_protobuf_protos/common.proto';
 
 package pw.protobuf.test;
diff --git a/pw_protobuf/pw_protobuf_protos/test_protos/non_pw_package.proto b/pw_protobuf/pw_protobuf_test_protos/non_pw_package.proto
similarity index 100%
rename from pw_protobuf/pw_protobuf_protos/test_protos/non_pw_package.proto
rename to pw_protobuf/pw_protobuf_test_protos/non_pw_package.proto
diff --git a/pw_protobuf/pw_protobuf_protos/test_protos/proto2.proto b/pw_protobuf/pw_protobuf_test_protos/proto2.proto
similarity index 100%
rename from pw_protobuf/pw_protobuf_protos/test_protos/proto2.proto
rename to pw_protobuf/pw_protobuf_test_protos/proto2.proto
diff --git a/pw_protobuf/pw_protobuf_protos/test_protos/repeated.proto b/pw_protobuf/pw_protobuf_test_protos/repeated.proto
similarity index 100%
rename from pw_protobuf/pw_protobuf_protos/test_protos/repeated.proto
rename to pw_protobuf/pw_protobuf_test_protos/repeated.proto
diff --git a/pw_protobuf_compiler/proto.gni b/pw_protobuf_compiler/proto.gni
index 03ff3c4..1478a64 100644
--- a/pw_protobuf_compiler/proto.gni
+++ b/pw_protobuf_compiler/proto.gni
@@ -230,25 +230,7 @@
 # file. Use pw_proto_library instead.
 template("_pw_python_proto_library") {
   _target = target_name
-  _package_dir = ""
-
-  foreach(_rebased_proto_path, rebase_path(invoker.sources, ".")) {
-    _path_components = []
-    _path_components = string_split(_rebased_proto_path, "/")
-
-    assert(_path_components != [ _rebased_proto_path ] &&
-               _path_components[0] != "..",
-           "Sources in a pw_proto_library must live in subdirectories " +
-               "of where it is defined")
-
-    if (_package_dir == "") {
-      _package_dir = _path_components[0]
-    } else {
-      assert(_path_components[0] == _package_dir,
-             "All .proto sources in a pw_proto_library must live " +
-                 "in the same directory tree")
-    }
-  }
+  _package_dir = invoker.package_dir
 
   _pw_invoke_protoc(target_name) {
     forward_variables_from(invoker, "*", _forwarded_vars)
@@ -261,7 +243,7 @@
   _generated_files = get_target_outputs(":$target_name._gen")
 
   # Create the setup and init files for the Python package.
-  pw_python_action(target_name + "._package_gen") {
+  action(target_name + "._package_gen") {
     script = "$dir_pw_protobuf_compiler/py/pw_protobuf_compiler/generate_python_package.py"
     args = [
              "--setup",
@@ -271,7 +253,7 @@
            ] + rebase_path(_generated_files, invoker.gen_dir)
 
     public_deps = [ ":$_target._gen" ]
-    stamp = true
+    outputs = [ _setup_py ]
   }
 
   # Create a Python package with the generated source files.
@@ -299,9 +281,36 @@
   assert(defined(invoker.sources) && invoker.sources != [],
          "pw_proto_library requires .proto source files")
 
+  _package_dir = ""
+
+  foreach(_rebased_proto_path, rebase_path(invoker.sources, ".")) {
+    _path_components = []
+    _path_components = string_split(_rebased_proto_path, "/")
+
+    assert(_path_components != [ _rebased_proto_path ] &&
+               _path_components[0] != "..",
+           "Sources in a pw_proto_library must live in subdirectories " +
+               "of where it is defined")
+
+    if (_package_dir == "") {
+      _package_dir = _path_components[0]
+    } else {
+      assert(_path_components[0] == _package_dir,
+             "All .proto sources in a pw_proto_library must live in the same " +
+                 "directory tree")
+    }
+  }
+
+  # Create a group with the package directory in the name. This prevents
+  # multiple pw_proto_libraries from generating the same setup.py file, which
+  # results in awkward ninja errors that require manually re-running gn gen.
+  group("pw_proto_library.$_package_dir") {
+    visibility = []
+  }
+
   _common = {
     base_target = target_name
-    gen_dir = "$target_gen_dir/protos"
+    gen_dir = "$target_gen_dir/$target_name"
     sources = invoker.sources
   }
 
@@ -393,6 +402,7 @@
     forward_variables_from(_common, "*")
     deps = process_file_template(_deps, "{{source}}.python")
     base_target = _common.base_target
+    package_dir = _package_dir
   }
 
   # All supported pw_protobuf generators.
diff --git a/pw_rpc/BUILD b/pw_rpc/BUILD
index aef8d1c..dfd0910 100644
--- a/pw_rpc/BUILD
+++ b/pw_rpc/BUILD
@@ -188,7 +188,7 @@
 proto_library(
     name = "packet_proto",
     srcs = [
-        "pw_rpc_protos/packet.proto",
+        "pw_rpc_protos/internal/packet.proto",
     ],
 )
 
diff --git a/pw_rpc/BUILD.gn b/pw_rpc/BUILD.gn
index 3e34b38..f25a335 100644
--- a/pw_rpc/BUILD.gn
+++ b/pw_rpc/BUILD.gn
@@ -16,6 +16,7 @@
 
 import("$dir_pw_bloat/bloat.gni")
 import("$dir_pw_build/module_config.gni")
+import("$dir_pw_build/python.gni")
 import("$dir_pw_build/python_action.gni")
 import("$dir_pw_build/target_types.gni")
 import("$dir_pw_docgen/docs.gni")
@@ -132,19 +133,23 @@
 }
 
 pw_proto_library("protos") {
-  sources = [ "pw_rpc_protos/packet.proto" ]
+  sources = [
+    "pw_rpc_protos/echo.proto",
+    "pw_rpc_protos/internal/packet.proto",
+  ]
+  inputs = [ "pw_rpc_protos/echo.options" ]
 }
 
-pw_proto_library("echo_service_proto") {
-  sources = [ "pw_rpc_protos/echo.proto" ]
-  inputs = [ "pw_rpc_protos/echo.options" ]
+# TODO(hepler): Remove this compatibility wrapper.
+pw_python_group("echo_service_proto.python") {
+  python_deps = [ ":protos.python" ]
 }
 
 pw_doc_group("docs") {
   sources = [ "docs.rst" ]
   inputs = [
     "pw_rpc_protos/echo.proto",
-    "pw_rpc_protos/packet.proto",
+    "pw_rpc_protos/internal/packet.proto",
   ]
   group_deps = [ "nanopb:docs" ]
   report_deps = [ ":server_size" ]
diff --git a/pw_rpc/CMakeLists.txt b/pw_rpc/CMakeLists.txt
index 5a892d1..cba62ca 100644
--- a/pw_rpc/CMakeLists.txt
+++ b/pw_rpc/CMakeLists.txt
@@ -69,11 +69,7 @@
 
 pw_proto_library(pw_rpc.protos
   SOURCES
-    pw_rpc_protos/packet.proto
-)
-
-pw_proto_library(pw_rpc.echo_proto
-  SOURCES
+    pw_rpc_protos/internal/packet.proto
     pw_rpc_protos/echo.proto
 )
 
diff --git a/pw_rpc/docs.rst b/pw_rpc/docs.rst
index 6681a87..7235232 100644
--- a/pw_rpc/docs.rst
+++ b/pw_rpc/docs.rst
@@ -238,9 +238,9 @@
 -------------
 Pigweed RPC packets consist of a type and a set of fields. The packets are
 encoded as protocol buffers. The full packet format is described in
-``pw_rpc/pw_rpc_protos/packet.proto``.
+``pw_rpc/pw_rpc_protos/internal/packet.proto``.
 
-.. literalinclude:: pw_rpc_protos/packet.proto
+.. literalinclude:: pw_rpc_protos/internal/packet.proto
   :language: protobuf
   :lines: 14-
 
diff --git a/pw_rpc/nanopb/BUILD.gn b/pw_rpc/nanopb/BUILD.gn
index 3b76625..c2e7788 100644
--- a/pw_rpc/nanopb/BUILD.gn
+++ b/pw_rpc/nanopb/BUILD.gn
@@ -86,7 +86,7 @@
 
 pw_source_set("echo_service") {
   public_configs = [ ":public" ]
-  public_deps = [ "..:echo_service_proto.nanopb_rpc" ]
+  public_deps = [ "..:protos.nanopb_rpc" ]
   sources = [ "public/pw_rpc/echo_service_nanopb.h" ]
 }
 
diff --git a/pw_rpc/nanopb/CMakeLists.txt b/pw_rpc/nanopb/CMakeLists.txt
index 896fefd..87552a0 100644
--- a/pw_rpc/nanopb/CMakeLists.txt
+++ b/pw_rpc/nanopb/CMakeLists.txt
@@ -52,7 +52,7 @@
 
 pw_add_module_library(pw_rpc.nanopb.echo_service
   PUBLIC_DEPS
-    pw_rpc.echo_proto.nanopb_rpc
+    pw_rpc.protos.nanopb_rpc
 )
 
 pw_auto_add_module_tests(pw_rpc.nanopb
@@ -61,7 +61,7 @@
     pw_rpc.raw
     pw_rpc.server
     pw_rpc.nanopb.common
-    pw_rpc.echo_proto.nanopb_rpc
+    pw_rpc.protos.nanopb_rpc
     pw_rpc.test_protos.nanopb_rpc
     pw_rpc.test_utils
 )
diff --git a/pw_rpc/public/pw_rpc/internal/packet.h b/pw_rpc/public/pw_rpc/internal/packet.h
index 9eb58a1..9ea3d7c 100644
--- a/pw_rpc/public/pw_rpc/internal/packet.h
+++ b/pw_rpc/public/pw_rpc/internal/packet.h
@@ -18,7 +18,7 @@
 #include <span>
 
 #include "pw_bytes/span.h"
-#include "pw_rpc_protos/packet.pwpb.h"
+#include "pw_rpc_protos/internal/packet.pwpb.h"
 #include "pw_status/status_with_size.h"
 
 namespace pw::rpc::internal {
diff --git a/pw_rpc/pw_rpc_protos/packet.proto b/pw_rpc/pw_rpc_protos/internal/packet.proto
similarity index 100%
rename from pw_rpc/pw_rpc_protos/packet.proto
rename to pw_rpc/pw_rpc_protos/internal/packet.proto
diff --git a/pw_rpc/py/callback_client_test.py b/pw_rpc/py/callback_client_test.py
index e9a675a..443b820 100755
--- a/pw_rpc/py/callback_client_test.py
+++ b/pw_rpc/py/callback_client_test.py
@@ -19,7 +19,7 @@
 from typing import List, Tuple
 
 from pw_protobuf_compiler import python_protos
-from pw_rpc_protos import packet_pb2
+from pw_rpc_protos.internal import packet_pb2
 from pw_status import Status
 
 from pw_rpc import callback_client, client, packets
diff --git a/pw_rpc/py/client_test.py b/pw_rpc/py/client_test.py
index 181bd0e..bcf3d06 100755
--- a/pw_rpc/py/client_test.py
+++ b/pw_rpc/py/client_test.py
@@ -16,7 +16,7 @@
 
 import unittest
 
-from pw_rpc_protos.packet_pb2 import RpcPacket
+from pw_rpc_protos.internal.packet_pb2 import RpcPacket
 from pw_protobuf_compiler import python_protos
 from pw_status import Status
 
diff --git a/pw_rpc/py/packets_test.py b/pw_rpc/py/packets_test.py
index acdd40a..ea49f3b 100755
--- a/pw_rpc/py/packets_test.py
+++ b/pw_rpc/py/packets_test.py
@@ -17,7 +17,7 @@
 import unittest
 
 from pw_status import Status
-from pw_rpc_protos.packet_pb2 import RpcPacket
+from pw_rpc_protos.internal.packet_pb2 import RpcPacket
 
 from pw_rpc import packets
 
diff --git a/pw_rpc/py/pw_rpc/client.py b/pw_rpc/py/pw_rpc/client.py
index c5ca88d..6c47ceb 100644
--- a/pw_rpc/py/pw_rpc/client.py
+++ b/pw_rpc/py/pw_rpc/client.py
@@ -19,7 +19,7 @@
 from typing import Collection, Dict, Iterable, Iterator, List, NamedTuple
 from typing import Optional
 
-from pw_rpc_protos.packet_pb2 import RpcPacket
+from pw_rpc_protos.internal.packet_pb2 import RpcPacket
 from pw_status import Status
 
 from pw_rpc import descriptors, packets
diff --git a/pw_rpc/py/pw_rpc/packets.py b/pw_rpc/py/pw_rpc/packets.py
index 6c53570..3ca6fbd 100644
--- a/pw_rpc/py/pw_rpc/packets.py
+++ b/pw_rpc/py/pw_rpc/packets.py
@@ -14,7 +14,7 @@
 """Functions for working with pw_rpc packets."""
 
 from google.protobuf import message
-from pw_rpc_protos import packet_pb2
+from pw_rpc_protos.internal import packet_pb2
 from pw_status import Status
 
 DecodeError = message.DecodeError
diff --git a/pw_target_runner/BUILD.gn b/pw_target_runner/BUILD.gn
index 6e67cbc..9db1016 100644
--- a/pw_target_runner/BUILD.gn
+++ b/pw_target_runner/BUILD.gn
@@ -27,5 +27,5 @@
 }
 
 pw_proto_library("exec_server_config_proto") {
-  sources = [ "pw_target_runner_protos/exec_server_config.proto" ]
+  sources = [ "pw_target_runner_server_protos/exec_server_config.proto" ]
 }
diff --git a/pw_target_runner/docs.rst b/pw_target_runner/docs.rst
index bca7084..28f20e9 100644
--- a/pw_target_runner/docs.rst
+++ b/pw_target_runner/docs.rst
@@ -39,7 +39,7 @@
 ^^^^^^^^^^^^^
 The standalone server is configured from a file written in Protobuf text format
 containing a ``pw.target_runner.ServerConfig`` message as defined in
-``//pw_target_runner/pw_target_runner_protos/exec_server_config.proto``.
+``//pw_target_runner/pw_target_runner_server_protos/exec_server_config.proto``.
 
 At least one ``worker`` message must be specified. Each of the workers refers to
 a script or program which is invoked with the path to an executable file as a
diff --git a/pw_target_runner/pw_target_runner_protos/exec_server_config.proto b/pw_target_runner/pw_target_runner_server_protos/exec_server_config.proto
similarity index 100%
rename from pw_target_runner/pw_target_runner_protos/exec_server_config.proto
rename to pw_target_runner/pw_target_runner_server_protos/exec_server_config.proto