diff --git a/src/main/kotlin/build/buf/gradle/DirectorySpecificBufExecutionSupport.kt b/src/main/kotlin/build/buf/gradle/DirectorySpecificBufExecutionSupport.kt
index cce488b5..0b800785 100644
--- a/src/main/kotlin/build/buf/gradle/DirectorySpecificBufExecutionSupport.kt
+++ b/src/main/kotlin/build/buf/gradle/DirectorySpecificBufExecutionSupport.kt
@@ -15,7 +15,7 @@
 package build.buf.gradle
 
 import org.gradle.api.Task
-import java.nio.file.Path
+import java.io.File
 
 internal fun Task.execBufInSpecificDirectory(
     vararg bufCommand: String,
@@ -37,12 +37,12 @@ private fun Task.execBufInSpecificDirectory(
     extraArgs: Iterable<String>,
     customErrorMessage: ((String) -> String)? = null
 ) {
-    fun runWithArgs(path: Path? = null) =
-        bufCommand + listOfNotNull(path?.let(::mangle)) + extraArgs
+    fun runWithArgs(file: File? = null) =
+        bufCommand + listOfNotNull(file?.let { project.makeMangledRelativizedPathStr(it) }) + extraArgs
 
     when {
         project.hasProtobufGradlePlugin() ->
-            project.srcProtoDirs().forEach { execBuf(runWithArgs(it), customErrorMessage) }
+            project.projectDefinedProtoDirs().forEach { execBuf(runWithArgs(it), customErrorMessage) }
         project.hasWorkspace() ->
             execBuf(bufCommand, customErrorMessage)
         else ->
diff --git a/src/main/kotlin/build/buf/gradle/ProtobufGradlePluginSupport.kt b/src/main/kotlin/build/buf/gradle/ProtobufGradlePluginSupport.kt
index 9d405fdc..fefa4bc6 100644
--- a/src/main/kotlin/build/buf/gradle/ProtobufGradlePluginSupport.kt
+++ b/src/main/kotlin/build/buf/gradle/ProtobufGradlePluginSupport.kt
@@ -58,7 +58,7 @@ abstract class CreateSymLinksToModulesTask : DefaultTask() {
     @TaskAction
     fun createSymLinksToModules() {
         allProtoDirs().forEach {
-            val symLinkFile = File(bufbuildDir, mangle(it))
+            val symLinkFile = File(bufbuildDir, project.makeMangledRelativizedPathStr(it))
             if (!symLinkFile.exists()) {
                 logger.info("Creating symlink for $it at $symLinkFile")
                 Files.createSymbolicLink(
@@ -102,15 +102,41 @@ private fun Task.workspaceCommonConfig() {
 }
 
 private fun Task.workspaceSymLinkEntries() =
-    allProtoDirs().joinToString("\n") { "|  - ${mangle(it)}" }
-
-private fun Task.allProtoDirs(): List<Path> =
-    (project.srcProtoDirs() + extractProtoDirs()).filter { project.anyProtos(it) }
+    allProtoDirs()
+        .map { project.makeMangledRelativizedPathStr(it) }
+        .joinToString("\n") { "|  - $it" }
+
+// Returns all directories that have may have proto files relevant to processing the project's proto files. This
+// includes any proto files that are simply references (includes) as well as those that will be processed (code
+// generation or validation).
+private fun Task.allProtoDirs() =
+    project.allProtoSourceSetDirs()
+        .plus(project.file(Paths.get(BUILD_EXTRACTED_INCLUDE_PROTOS_MAIN)))
+        .filter { anyProtos(it) }
+        .toSet()
+
+// Returns the list of directories containing proto files defined in *this* project. The returned directories do *not*
+// include those that contain protos defined in dependencies and placed in the extracted-protos directory for codegen.
+// The returned directories *only* contain the proto files that should be processed by buf for operations like linting,
+// format checking, and breaking change detection.
+//
+// NOTE: We explicitly remove BUILD_EXTRACTED_PROTOS_MAIN from the list of source set directories in order to fix issue
+// https://github.com/bufbuild/buf-gradle-plugin/issues/132. Starting in version 0.9.2 of
+// protobuf-gradle-plugin, the "proto" source set srcDirs includes the outputs of the "extractedProtos" task, which
+// breaks this plugin when used with the protobuf-gradle-plugin and "protobuf" dependencies (which generates code for
+// any proto files within those dependencies).
+//
+// Protobuf-gradle-plugin change that introduced this behavior: https://github.com/google/protobuf-gradle-plugin/pull/637/
+// Line: https://github.com/google/protobuf-gradle-plugin/blob/9d2a328a0d577bf4439d3b482a953715b3a03027/src/main/groovy/com/google/protobuf/gradle/ProtobufPlugin.groovy#L425
+internal fun Project.projectDefinedProtoDirs() =
+    allProtoSourceSetDirs() - file(Paths.get(BUILD_EXTRACTED_PROTOS_MAIN))
 
-internal fun Project.srcProtoDirs() =
-    the<SourceSetContainer>().flatMap { it.protoDirs(this) } + androidSrcProtoDirs()
+// Returns deduplicated list of all proto source set directories.
+private fun Project.allProtoSourceSetDirs() =
+    projectProtoSourceSetDirs() + androidProtoSourceSetDirs()
 
-private fun Project.androidSrcProtoDirs() =
+// Returns android proto source set directories that protobuf-gradle-plugin will codegen.
+private fun Project.androidProtoSourceSetDirs() =
     extensions.findByName("android")
         ?.let { baseExtension ->
             val prop = baseExtension::class.declaredMemberProperties.single { it.name == "sourceSets" }
@@ -118,23 +144,29 @@ private fun Project.androidSrcProtoDirs() =
             (prop as KProperty1<Any, Set<ExtensionAware>>).get(baseExtension)
         }
         .orEmpty()
-        .flatMap { it.protoDirs(this) }
+        .flatMap { it.projectProtoSourceSetDirs() }
+        .toSet()
+
+// Returns all proto source set directories that the protobuf-gradle-plugin will codegen.
+private fun Project.projectProtoSourceSetDirs() =
+    the<SourceSetContainer>().flatMap { it.projectProtoSourceSetDirs() }
+        .toSet()
 
-private fun ExtensionAware.protoDirs(project: Project) =
+// Returns all directories within the "proto" source set of the receiver that actually contain proto files. This includes
+// directories explicitly added to the source set, as well as directories containing files from "protobuf" dependencies.
+private fun ExtensionAware.projectProtoSourceSetDirs() =
     extensions.getByName<SourceDirectorySet>("proto").srcDirs
-        .map { project.projectDir.toPath().relativize(it.toPath()) }
-        .filter { project.anyProtos(it) }
+        .filter { anyProtos(it) }
+        .toSet()
 
-private fun extractProtoDirs() =
-    listOf(
-        BUILD_EXTRACTED_INCLUDE_PROTOS_MAIN,
-        BUILD_EXTRACTED_PROTOS_MAIN
-    ).map(Paths::get)
+internal fun Project.makeMangledRelativizedPathStr(file: File) =
+    mangle(projectDir.toPath().relativize(file.toPath()))
 
-private fun Project.anyProtos(path: Path) =
-    file(path).walkTopDown().any { it.extension == "proto" }
+// Indicates if the specified directory contains any proto files.
+private fun anyProtos(directory: File) =
+    directory.walkTopDown().any { it.extension == "proto" }
 
-internal fun mangle(name: Path) =
+private fun mangle(name: Path) =
     name.toString().replace("-", "--").replace(File.separator, "-")
 
 internal inline fun <reified T : Task> Project.registerBufTask(
diff --git a/src/test/kotlin/build/buf/gradle/AbstractBufIntegrationTest.kt b/src/test/kotlin/build/buf/gradle/AbstractBufIntegrationTest.kt
index 855aec8c..039a2ae7 100644
--- a/src/test/kotlin/build/buf/gradle/AbstractBufIntegrationTest.kt
+++ b/src/test/kotlin/build/buf/gradle/AbstractBufIntegrationTest.kt
@@ -71,7 +71,7 @@ abstract class AbstractBufIntegrationTest : IntegrationTest {
             .withProjectDir(projectDir)
             .withPluginClasspath()
             .withArguments(
-                "-PprotobufGradleVersion=0.8.19",
+                "-PprotobufGradleVersion=0.9.3",
                 "-PprotobufVersion=3.21.7",
                 "-PkotlinVersion=1.7.20",
                 "-PandroidGradleVersion=7.3.0"