diff --git a/plugin/src/main/java/org/openrewrite/gradle/RewritePlugin.java b/plugin/src/main/java/org/openrewrite/gradle/RewritePlugin.java
index 1549446dd..16c9534eb 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/RewritePlugin.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/RewritePlugin.java
@@ -118,7 +118,7 @@ private static void configureProject(Project project, RewriteExtension extension
                             return 2;
                         }
                     })).forEach(sourceSet -> {
-                        for (File file : sourceSet.getAllSource().getSourceDirectories().getFiles()) {
+                        for (File file : sourceSet.getAllJava().getSourceDirectories().getFiles()) {
                             if (!sourceDirs.add(file.getAbsolutePath())) {
                                 Task compileTask = project.getTasks().getByPath(sourceSet.getCompileJavaTaskName());
                                 compileTask.setEnabled(false);
diff --git a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
index bc8d72ce9..5f2819049 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
@@ -85,6 +85,7 @@
 import java.util.function.Consumer;
 import java.util.function.Supplier;
 import java.util.function.UnaryOperator;
+import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
 import static java.util.Collections.*;
@@ -653,15 +654,7 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
             }
 
             Set<String> sourceDirs = new HashSet<>();
-            sourceSetLoop:
             for (SourceSet sourceSet : sourceSets) {
-                        // Detect SourceSets which overlap other sourceSets and disable the compilation task of the overlapping
-            // source set. Skip parsing directories already covered by another source set.
-                for (File file : sourceSet.getAllSource().getSourceDirectories().getFiles()) {
-                    if (!sourceDirs.add(file.getAbsolutePath())) {
-                        continue sourceSetLoop;
-                    }
-                }
                 Stream<SourceFile> sourceSetSourceFiles = Stream.of();
                 int sourceSetSize = 0;
 
@@ -672,11 +665,24 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
                         javaCompileTask.getSourceCompatibility(),
                         javaCompileTask.getTargetCompatibility());
 
-                List<Path> javaPaths = sourceSet.getAllJava().getFiles().stream()
-                        .filter(it -> it.isFile() && it.getName().endsWith(".java"))
-                        .map(File::toPath)
+                List<Path> unparsedSources = sourceSet.getAllSource()
+                        .getSourceDirectories()
+                        .filter(it -> it.exists() && !alreadyParsed.contains(baseDir.relativize(it.toPath())))
+                        .getFiles()
+                        .stream()
+                        .flatMap(sourceDir -> {
+                            try {
+                                return Files.walk(sourceDir.toPath());
+                            } catch (IOException e) {
+                                throw new UncheckedIOException(e);
+                            }
+                        })
+                        .filter(Files::isRegularFile)
                         .map(Path::toAbsolutePath)
                         .map(Path::normalize)
+                        .collect(Collectors.toList());
+                List<Path> javaPaths = unparsedSources.stream()
+                        .filter(it -> it.toString().endsWith(".java"))
                         .collect(toList());
 
                 // classpath doesn't include the transitive dependencies of the implementation configuration
@@ -731,11 +737,8 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
                 }
 
                 if (subproject.getPlugins().hasPlugin("org.jetbrains.kotlin.jvm")) {
-                    List<Path> kotlinPaths = sourceSet.getAllSource().getFiles().stream()
-                            .filter(it -> it.isFile() && it.getName().endsWith(".kt"))
-                            .map(File::toPath)
-                            .map(Path::toAbsolutePath)
-                            .map(Path::normalize)
+                    List<Path> kotlinPaths = unparsedSources.stream()
+                            .filter(it -> it.toString().endsWith(".kt"))
                             .collect(toList());
 
                     if (!kotlinPaths.isEmpty()) {
@@ -762,13 +765,9 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
                         logger.info("Scanned {} Kotlin sources in {}/{}", kotlinPaths.size(), subproject.getPath(), sourceSet.getName());
                     }
                 }
-
                 if (subproject.getPlugins().hasPlugin(GroovyPlugin.class)) {
-                    List<Path> groovyPaths = sourceSet.getAllSource().getFiles().stream()
-                            .filter(it -> it.isFile() && it.getName().endsWith(".groovy"))
-                            .map(File::toPath)
-                            .map(Path::toAbsolutePath)
-                            .map(Path::normalize)
+                    List<Path> groovyPaths = unparsedSources.stream()
+                            .filter(it -> it.toString().endsWith(".groovy"))
                             .collect(toList());
 
                     if (!groovyPaths.isEmpty()) {
@@ -805,7 +804,7 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
                 }
 
                 for (File resourcesDir : sourceSet.getResources().getSourceDirectories()) {
-                    if (resourcesDir.exists()) {
+                    if (resourcesDir.exists() && !alreadyParsed.contains(baseDir.relativize(resourcesDir.toPath()))) {
                         OmniParser omniParser = omniParser(alreadyParsed);
                         List<Path> accepted = omniParser.acceptedPaths(baseDir, resourcesDir.toPath());
                         sourceSetSourceFiles = Stream.concat(
@@ -819,6 +818,11 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
 
                 JavaSourceSet sourceSetProvenance = JavaSourceSet.build(sourceSet.getName(), dependencyPaths, javaTypeCache, false);
                 sourceFileStream = sourceFileStream.concat(sourceSetSourceFiles.map(addProvenance(sourceSetProvenance)), sourceSetSize);
+                // Some source sets get misconfigured to have the same directories as other source sets
+                // This causes duplicate source files to be parsed, so once a source set has been parsed exclude it from future parsing
+                for (File file : sourceSet.getAllSource().getSourceDirectories().getFiles()) {
+                    alreadyParsed.add(baseDir.relativize(file.toPath()));
+                }
             }
             SourceFileStream gradleFiles = parseGradleFiles(exclusions, alreadyParsed, ctx);
             sourceFileStream = sourceFileStream.concat(gradleFiles, gradleFiles.size());
diff --git a/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt b/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt
index d77f32793..8aee56aaa 100644
--- a/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt
+++ b/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt
@@ -40,7 +40,7 @@ class RewriteRunTest : RewritePluginTest {
         // Gradle provides no control over how it arbitrarily orders its classpath
         // So even if isolation isn't working at all, this could pass if it happens to put the rewrite's required version
         // of jackson first on the classpath.
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             buildGradle("""
                 buildscript {
                     repositories {
@@ -69,7 +69,7 @@ class RewriteRunTest : RewritePluginTest {
                     activeRecipe("org.openrewrite.java.format.AutoFormat")
                 }
             """)
-            sourceSet("test") { 
+            sourceSet("test") {
                 java("""
                     package com.foo;
                     
@@ -89,7 +89,7 @@ class RewriteRunTest : RewritePluginTest {
     fun `rewriteRun will alter the source file according to the provided active recipe`(
         @TempDir projectDir: File
     ) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/recipe
                 name: org.openrewrite.gradle.SayHello
@@ -119,7 +119,7 @@ class RewriteRunTest : RewritePluginTest {
                     activeRecipe("org.openrewrite.gradle.SayHello", "org.openrewrite.java.format.AutoFormat")
                 }
             """)
-            sourceSet("main") { 
+            sourceSet("main") {
                 java("""
                     package org.openrewrite.before;
                     
@@ -170,7 +170,7 @@ class RewriteRunTest : RewritePluginTest {
                     public void passes() { }
                 }
         """.trimIndent()
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/recipe
                 name: org.openrewrite.FormatAndAddProperty
@@ -212,8 +212,8 @@ class RewriteRunTest : RewritePluginTest {
                     }
                 }
             """)
-            subproject("a") { 
-                sourceSet("test") { 
+            subproject("a") {
+                sourceSet("test") {
                     java("""
                         package com.foo;
             
@@ -228,8 +228,8 @@ class RewriteRunTest : RewritePluginTest {
                     propertiesFile("test.properties", "foo=baz\n")
                 }
             }
-            subproject("b") { 
-                sourceSet("test") { 
+            subproject("b") {
+                sourceSet("test") {
                     java(bTestClassExpected)
                 }
             }
@@ -265,7 +265,7 @@ class RewriteRunTest : RewritePluginTest {
     fun `Checkstyle configuration is applied as a style`(
         @TempDir projectDir: File
     ) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             checkstyleXml("""
                 <!DOCTYPE module PUBLIC
                     "-//Checkstyle//DTD Checkstyle Configuration 1.2//EN"
@@ -299,7 +299,7 @@ class RewriteRunTest : RewritePluginTest {
                     rewrite("org.openrewrite.recipe:rewrite-static-analysis:1.0.4")
                 }
             """)
-            sourceSet("main") { 
+            sourceSet("main") {
                 java("""
                     package com.foo;
                     
@@ -338,7 +338,7 @@ class RewriteRunTest : RewritePluginTest {
     fun `can apply non-java recipe to files inside and outside of java resources directories`(
         @TempDir projectDir: File
     ) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/recipe
                 name: com.example.RenameSam
@@ -368,7 +368,7 @@ class RewriteRunTest : RewritePluginTest {
                 }
             """)
             propertiesFile("outside-of-sourceset.properties", "sam=true\n")
-            sourceSet("main") { 
+            sourceSet("main") {
                 propertiesFile("in-sourceset.properties", "sam=true\n")
             }
         }
@@ -385,7 +385,7 @@ class RewriteRunTest : RewritePluginTest {
     fun `Recipes that generate sources have those sources written out to disk successfully`(
         @TempDir projectDir: File
     ) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/recipe
                 name: org.openrewrite.test.AddGradleWrapper
@@ -442,7 +442,7 @@ class RewriteRunTest : RewritePluginTest {
     fun gradleDependencyManagement(
         @TempDir projectDir: File
     ) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/recipe
                 name: org.openrewrite.test.RemoveJacksonCore
@@ -518,7 +518,7 @@ class RewriteRunTest : RewritePluginTest {
 
     @Test
     fun mergeConfiguredAndAutodetectedStyles(@TempDir projectDir: File) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             propertiesFile("gradle.properties", "systemProp.rewrite.activeStyles=org.openrewrite.testStyle")
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/style
@@ -545,7 +545,7 @@ class RewriteRunTest : RewritePluginTest {
                     activeRecipe("org.openrewrite.java.format.AutoFormat")
                 }
             """)
-            sourceSet("main") { 
+            sourceSet("main") {
                 // Uses spaces, to be converted to tabs
                 java("""
                     package com.foo;
@@ -588,7 +588,7 @@ class RewriteRunTest : RewritePluginTest {
 
     @Test
     fun reformatToIntelliJStyle(@TempDir projectDir: File) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             buildGradle("""
                 plugins {
                     id("java")
@@ -608,7 +608,7 @@ class RewriteRunTest : RewritePluginTest {
                     activeStyle("org.openrewrite.java.IntelliJ")
                 }
             """)
-            sourceSet("main") { 
+            sourceSet("main") {
                 java("""
                     package com.foo;
                     
@@ -663,7 +663,7 @@ class RewriteRunTest : RewritePluginTest {
 
     @Test
     fun groovySourceGetsTypesFromJavaSource(@TempDir projectDir: File) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/recipe
                 name: org.openrewrite.test.FindA
@@ -696,7 +696,7 @@ class RewriteRunTest : RewritePluginTest {
                 }
                 
             """)
-            sourceSet("main") { 
+            sourceSet("main") {
                 java("""
                     package com.foo;
                     
@@ -738,7 +738,7 @@ class RewriteRunTest : RewritePluginTest {
     @DisabledIf("lessThanGradle6_1")
     @Test
     fun kotlinSource(@TempDir projectDir: File) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             buildGradle(
                 """
                 plugins {
@@ -765,7 +765,7 @@ class RewriteRunTest : RewritePluginTest {
                   - org.openrewrite.java.search.FindTypes:
                       fullyQualifiedTypeName: kotlin.String
             """)
-            sourceSet("main") { 
+            sourceSet("main") {
                 kotlin("""
                     package com.foo
                     
@@ -789,7 +789,7 @@ class RewriteRunTest : RewritePluginTest {
     @Issue("https://github.com/openrewrite/rewrite-gradle-plugin/issues/128")
     @Test
     fun deleteEmptyDirectory(@TempDir projectDir: File) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             rewriteYaml("""
               type: specs.openrewrite.org/v1beta/recipe
               name: org.openrewrite.test.DeleteFoo
@@ -836,26 +836,26 @@ class RewriteRunTest : RewritePluginTest {
 
     @Test
     fun `build root and repository root do not need to be the same`(@TempDir repositoryRoot: File) {
-        repositoryRoot.apply{ 
-            resolve(".git").apply{ 
+        repositoryRoot.apply{
+            resolve(".git").apply{
                 mkdirs()
-                resolve("HEAD").apply{ 
+                resolve("HEAD").apply{
                     createNewFile()
                     writeText("ref: refs/heads/main")
                 }
-                resolve("objects").apply{ 
+                resolve("objects").apply{
                     mkdir()
                 }
-                resolve("refs").apply{ 
+                resolve("refs").apply{
                     mkdir()
                 }
-                resolve("reftable").apply{ 
+                resolve("reftable").apply{
                     mkdir()
                 }
             }
         }
         val buildRoot = repositoryRoot.resolve("test-project").apply{  mkdirs() }
-        gradleProject(buildRoot) { 
+        gradleProject(buildRoot) {
             buildGradle("""
                 plugins {
                     id("java")
@@ -874,7 +874,7 @@ class RewriteRunTest : RewritePluginTest {
                     activeRecipe("org.openrewrite.java.format.AutoFormat")
                 }
             """)
-            sourceSet("main") { 
+            sourceSet("main") {
                 java("""
                     package org.openrewrite.before;
                 
@@ -918,20 +918,20 @@ class RewriteRunTest : RewritePluginTest {
     @Issue("https://github.com/openrewrite/rewrite-gradle-plugin/issues/176")
     @Test
     fun runRecipeFromProjectDependency(@TempDir projectDir: File) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             settingsGradle("""
                 rootProject.name = 'multi-project-recipe'
 
                 include("recipe")
                 include("product")
             """)
-            subproject("recipe") { 
+            subproject("recipe") {
                 buildGradle("""
                     plugins { 
                         id("java")
                     }
                 """)
-                sourceSet("main") { 
+                sourceSet("main") {
                     yamlFile("META-INF/rewrite/recipe.yml", """
                         type: specs.openrewrite.org/v1beta/recipe
                         name: com.example.TextToSam
@@ -947,7 +947,7 @@ class RewriteRunTest : RewritePluginTest {
                     """)
                 }
             }
-            subproject("product") { 
+            subproject("product") {
                 buildGradle("""
                     plugins {
                         id("org.openrewrite.rewrite")
@@ -988,15 +988,16 @@ class RewriteRunTest : RewritePluginTest {
 
     @Test
     fun overlappingSourceSet(@TempDir buildRoot: File) {
-        gradleProject(buildRoot) { 
+        gradleProject(buildRoot) {
             rewriteYaml("""
               type: specs.openrewrite.org/v1beta/recipe
-              name: org.openrewrite.test.FindSneaky
-              displayName: Find lombok SneakyThrows annotation
-              description: Find lombok SneakyThrows annotation
+              name: org.openrewrite.Overlaps
+              displayName: Find overlaps
+              description: Find lombok SneakyThrows annotation and duplicate source files
               recipeList:
                 - org.openrewrite.java.search.FindTypes:
                     fullyQualifiedTypeName: lombok.SneakyThrows
+                - org.openrewrite.FindDuplicateSourceFiles
             """)
             buildGradle("""
                 plugins { 
@@ -1017,16 +1018,17 @@ class RewriteRunTest : RewritePluginTest {
                         java.srcDir("src/test/java")
                     }
                 }
-                
+
                 rewrite {
-                    activeRecipe("org.openrewrite.test.FindSneaky")
+                    activeRecipe("org.openrewrite.Overlaps")
                 }
                 
                 dependencies {
+                    rewrite("org.openrewrite.recipe:rewrite-all:latest.integration")
                     testImplementation("org.projectlombok:lombok:latest.release")
                 }
             """)
-            sourceSet("test") { 
+            sourceSet("test") {
                 java("""
                     package com.foo;