diff --git a/.bazelci/presubmit.yml b/.bazelci/presubmit.yml
index 0244f63..387dffc 100644
--- a/.bazelci/presubmit.yml
+++ b/.bazelci/presubmit.yml
@@ -5,16 +5,9 @@
     - ubuntu2004
     - macos
 
-.incompatible_flags: &incompatible_flags
-  ? "--config=incompatible"
-
 .noenable_bzlmod_flags: &noenable_bzlmod_flags
   ? "--noenable_bzlmod"
 
-.incompatible_noenable_bzlmod_flags: &incompatible_noenable_bzlmod_flags
-  ? "--config=incompatible"
-  ? "--noenable_bzlmod"
-
 .windows_flags: &windows_flags
   # Workaround for https://github.com/bazelbuild/continuous-integration/issues/1012
   ? "--noexperimental_repository_cache_hardlinks"
@@ -25,11 +18,6 @@
   test_targets:
     - "//..."
 
-.incompatible_task_config: &incompatible_task_config
-  <<: *common_task_config
-  build_flags: *incompatible_flags
-  test_flags: *incompatible_flags
-
 .noenable_bzlmod_task_config: &noenable_bzlmod_task_config
   build_flags: *noenable_bzlmod_flags
   build_targets:
@@ -46,11 +34,6 @@
     - "//test:table_of_contents_noenable_bzlmod_test"
     - "//test:local_repository_test"
 
-.incompatible_noenable_bzlmod_task_config: &incompatible_noenable_bzlmod_task_config
-  <<: *noenable_bzlmod_task_config
-  build_flags: *incompatible_noenable_bzlmod_flags
-  test_flags: *incompatible_noenable_bzlmod_flags
-
 .windows_task_config: &windows_task_config
   <<: *common_task_config
   build_flags: *windows_flags
@@ -62,11 +45,6 @@
     name: Build and test
     platform: ${{ platform }}
 
-  build_and_test_incompatible:
-    <<: *incompatible_task_config
-    name: Build and test - incompatible flags
-    platform: ${{ platform }}
-
   build_and_test_windows:
     <<: *windows_task_config
     name: Build and test - Windows
@@ -77,11 +55,6 @@
     name: Build and test - legacy WORKSPACE setup
     platform: ${{ platform }}
 
-  incompatible_noenable_bzlmod:
-    <<: *incompatible_noenable_bzlmod_task_config
-    name: Build and test - legacy WORKSPACE setup with incompatible flags
-    platform: ${{ platform }}
-
   build_and_test_last_green:
     <<: *common_task_config
     name: Build and test - Bazel last green
@@ -100,12 +73,6 @@
     platform: ${{ platform }}
     working_directory: test/bzlmod
 
-  bzlmod_usage_incompatible:
-    <<: *incompatible_task_config
-    name: Stardoc Bzlmod module usage test - incompatible flags
-    platform: ${{ platform }}
-    working_directory: test/bzlmod
-
   bzlmod_usage_windows:
     <<: *windows_task_config
     name: Stardoc Bzlmod module usage test - Windows
diff --git a/.bazelrc b/.bazelrc
index 33808dd..b968cdc 100644
--- a/.bazelrc
+++ b/.bazelrc
@@ -4,6 +4,3 @@
 # Incompatible flags which we always want in development
 build --incompatible_disable_starlark_host_transitions
 build --incompatible_disallow_empty_glob
-
-# Incompatible flags to test in a dedicated CI pipeline.
-build:incompatible --incompatible_enable_proto_toolchain_resolution
diff --git a/MODULE.bazel b/MODULE.bazel
index 772f583..6fe8c48 100644
--- a/MODULE.bazel
+++ b/MODULE.bazel
@@ -9,8 +9,6 @@
 bazel_dep(name = "rules_java", version = "7.6.1")
 bazel_dep(name = "rules_jvm_external", version = "6.1")
 bazel_dep(name = "rules_license", version = "0.0.7")
-bazel_dep(name = "rules_proto", version = "6.0.2")
-bazel_dep(name = "toolchains_protoc", version = "0.3.1")
 
 # Maven artifacts required by Stardoc; keep consistent with deps.bzl
 STARDOC_MAVEN_ARTIFACTS = [
@@ -19,7 +17,6 @@
     "com.google.guava:guava:31.1-jre",
     "com.google.truth:truth:1.1.3",
     "junit:junit:4.13.2",
-    "com.google.protobuf:protobuf-java:4.27.1",
 ]
 
 maven = use_extension("@rules_jvm_external//:extensions.bzl", "maven")
@@ -39,5 +36,3 @@
 #
 # Dev-only and test-only dependencies
 bazel_dep(name = "rules_pkg", version = "0.10.1", dev_dependency = True)
-
-register_toolchains("//toolchains:all")
diff --git a/WORKSPACE b/WORKSPACE
index d7e67ac..a8f1d4c 100644
--- a/WORKSPACE
+++ b/WORKSPACE
@@ -67,12 +67,15 @@
 
 rules_pkg_dependencies()
 
-# Needed as a transitive dependency of @io_bazel
-http_archive(
-    name = "rules_proto",
-    sha256 = "6fb6767d1bef535310547e03247f7518b03487740c11b6c6adb7952033fe1295",
-    strip_prefix = "rules_proto-6.0.2",
-    url = "https://github.com/bazelbuild/rules_proto/releases/download/6.0.2/rules_proto-6.0.2.tar.gz",
+# Needed only for testing stardoc across local-repository bounds.
+local_repository(
+    name = "stardoc",  # alias the Bzlmod name of the Stardoc repo for local_repository_test
+    path = ".",
+)
+
+local_repository(
+    name = "local_repository_test",
+    path = "test/testdata/local_repository_test",
 )
 
 load("@rules_proto//proto:repositories.bzl", "rules_proto_dependencies")
@@ -86,27 +89,3 @@
 load("@rules_proto//proto:toolchains.bzl", "rules_proto_toolchains")
 
 rules_proto_toolchains()
-
-load("@bazel_features//:deps.bzl", "bazel_features_deps")
-
-bazel_features_deps()
-
-load("@toolchains_protoc//protoc:toolchain.bzl", "protoc_toolchains")
-
-protoc_toolchains(
-    name = "protoc_toolchains",
-    version = "v27.1",
-)
-
-# Needed only for testing stardoc across local-repository bounds.
-local_repository(
-    name = "stardoc",  # alias the Bzlmod name of the Stardoc repo for local_repository_test
-    path = ".",
-)
-
-local_repository(
-    name = "local_repository_test",
-    path = "test/testdata/local_repository_test",
-)
-
-register_toolchains("//toolchains:all")
diff --git a/deps.bzl b/deps.bzl
index 35574b7..647a3cd 100644
--- a/deps.bzl
+++ b/deps.bzl
@@ -16,6 +16,8 @@
 
 load("@com_google_protobuf//:protobuf_deps.bzl", "protobuf_deps")
 load("@rules_jvm_external//:defs.bzl", "maven_install")
+load("@rules_proto//proto:repositories.bzl", "rules_proto_dependencies")
+load("@rules_proto//proto:setup.bzl", "rules_proto_setup")
 
 # Maven artifacts required by Stardoc; keep consistent with MODULE.bazel
 STARDOC_MAVEN_ARTIFACTS = [
@@ -24,7 +26,6 @@
     "com.google.guava:guava:31.1-jre",
     "com.google.truth:truth:1.1.3",
     "junit:junit:4.13.2",
-    "com.google.protobuf:protobuf-java:4.27.1",
 ]
 
 def stardoc_external_deps():
@@ -41,8 +42,6 @@
         stardoc_pinned_maven_install()
     ```
     """
-    protobuf_deps()
-
     maven_install(
         name = "stardoc_maven",
         artifacts = STARDOC_MAVEN_ARTIFACTS,
@@ -53,3 +52,10 @@
         ],
         strict_visibility = True,
     )
+
+    protobuf_deps()
+
+    rules_proto_dependencies()
+
+    # Note rules_proto_setup() requires @bazel_features - we define it in stardoc_repositories()
+    rules_proto_setup()
diff --git a/maven_install.json b/maven_install.json
index a3a69ae..3706219 100644
--- a/maven_install.json
+++ b/maven_install.json
@@ -1,7 +1,7 @@
 {
   "__AUTOGENERATED_FILE_DO_NOT_MODIFY_THIS_FILE_MANUALLY": "THERE_IS_NO_DATA_ONLY_ZUUL",
-  "__INPUT_ARTIFACTS_HASH": 1794655755,
-  "__RESOLVED_ARTIFACTS_HASH": 2130017368,
+  "__INPUT_ARTIFACTS_HASH": -1307151106,
+  "__RESOLVED_ARTIFACTS_HASH": 1764595048,
   "artifacts": {
     "com.beust:jcommander": {
       "shasums": {
@@ -57,12 +57,6 @@
       },
       "version": "1.3"
     },
-    "com.google.protobuf:protobuf-java": {
-      "shasums": {
-        "jar": "798c79f6c9fc6859cc76aa5474228aad250821438e1004dad34880d53aa745f9"
-      },
-      "version": "4.27.1"
-    },
     "com.google.truth:truth": {
       "shasums": {
         "jar": "fc0b67782289a2aabfddfdf99eff1dcd5edc890d49143fcd489214b107b8f4f3"
@@ -172,10 +166,6 @@
     "com.google.j2objc:j2objc-annotations": [
       "com.google.j2objc.annotations"
     ],
-    "com.google.protobuf:protobuf-java": [
-      "com.google.protobuf",
-      "com.google.protobuf.compiler"
-    ],
     "com.google.truth:truth": [
       "com.google.common.truth"
     ],
@@ -265,7 +255,6 @@
       "com.google.guava:guava",
       "com.google.guava:listenablefuture",
       "com.google.j2objc:j2objc-annotations",
-      "com.google.protobuf:protobuf-java",
       "com.google.truth:truth",
       "junit:junit",
       "org.checkerframework:checker-qual",
@@ -273,5 +262,6 @@
       "org.ow2.asm:asm"
     ]
   },
+  "services": {},
   "version": "2"
 }
diff --git a/setup.bzl b/setup.bzl
index 985c2b3..9ebab24 100644
--- a/setup.bzl
+++ b/setup.bzl
@@ -70,14 +70,6 @@
         sha256 = "4531deccb913639c30e5c7512a054d5d875698daeb75d8cf90f284375fe7c360",
     )
 
-    maybe(
-        http_archive,
-        name = "toolchains_protoc",
-        sha256 = "3898f8e621ca5b3c7b94300c5ae19075d5bb28349d6e6f407490a466ba1e2544",
-        strip_prefix = "toolchains_protoc-0.3.1",
-        url = "https://github.com/aspect-build/toolchains_protoc/releases/download/v0.3.1/toolchains_protoc-v0.3.1.tar.gz",
-    )
-
     # Transitive dep of com_google_protobuf. Unfortunately, protobuf_deps()
     # pulls in a dep that's too old.
     maybe(
@@ -88,6 +80,17 @@
         url = "https://github.com/bazelbuild/rules_proto/releases/download/6.0.2/rules_proto-6.0.2.tar.gz",
     )
 
+    # Transitive dep of rules_proto. Pull in explicitly to allow calling both
+    # rules_proto_dependencies() and rules_proto_setup() in stardoc_external_deps() without forcing
+    # users to add yet another intermediate load() in their WORKSPACE files.
+    maybe(
+        http_archive,
+        name = "bazel_features",
+        sha256 = "0f23d75c7623d6dba1fd30513a94860447de87c8824570521fcc966eda3151c2",
+        strip_prefix = "bazel_features-1.4.1",
+        url = "https://github.com/bazel-contrib/bazel_features/releases/download/v1.4.1/bazel_features-v1.4.1.tar.gz",
+    )
+
     # Transitive dep of com_google_protobuf. Unfortunately, protobuf_deps()
     # pulls in a dep that's too old.
     maybe(
diff --git a/test/bzlmod/.bazelrc b/test/bzlmod/.bazelrc
index 305a751..7a949e8 100644
--- a/test/bzlmod/.bazelrc
+++ b/test/bzlmod/.bazelrc
@@ -6,5 +6,3 @@
 build --incompatible_disable_starlark_host_transitions
 build --incompatible_disallow_empty_glob
 
-# Incompatible flags to test in a dedicated CI pipeline.
-build:incompatible --incompatible_enable_proto_toolchain_resolution
diff --git a/toolchains/BUILD.bazel b/toolchains/BUILD.bazel
deleted file mode 100644
index 3e02065..0000000
--- a/toolchains/BUILD.bazel
+++ /dev/null
@@ -1,12 +0,0 @@
-proto_lang_toolchain(
-    name = "protoc_java_toolchain",
-    command_line = "--java_out=%s",
-    progress_message = "Generating Java proto_library %{label}",
-    runtime = "@stardoc_maven//:com_google_protobuf_protobuf_java",
-)
-
-toolchain(
-    name = "protoc_java_toolchain.registration",
-    toolchain = ":protoc_java_toolchain",
-    toolchain_type = "@rules_java//java/proto:toolchain_type",
-)