diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/Kapt3IT.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/Kapt3IT.kt
index 13c184b585e..016b2c4418a 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/Kapt3IT.kt
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/Kapt3IT.kt
@@ -16,6 +16,7 @@
 
 package org.jetbrains.kotlin.gradle
 
+import org.gradle.api.logging.LogLevel
 import org.gradle.api.logging.configuration.WarningMode
 import org.jetbrains.kotlin.gradle.tasks.USING_JVM_INCREMENTAL_COMPILATION_MESSAGE
 import org.jetbrains.kotlin.gradle.util.*
@@ -783,4 +784,37 @@ open class Kapt3IT : Kapt3BaseIT() {
 
         }
     }
+
+    // https://youtrack.jetbrains.com/issue/KT-46651
+    @Test
+    fun kaptGenerateStubsShouldNotCaptureSourcesStateInConfigurationCache() {
+        with(
+            Project(
+                "incrementalRebuild",
+                directoryPrefix = "kapt2",
+                gradleVersionRequirement = GradleVersionRequired.AtLeast("6.7.1"),
+                minLogLevel = LogLevel.INFO
+            )
+        ) {
+            setupWorkingDir()
+            val buildOptions = defaultBuildOptions().copy(
+                configurationCache = true
+            )
+
+            build("assemble", options = buildOptions) {
+                assertSuccessful()
+            }
+
+            projectDir.resolve("src/main/java/bar/UseBar.kt").apply {
+                modify {
+                    it.replace("UseBar", "UseBar1")
+                }
+                renameTo(parentFile.resolve("UseBar1.kt"))
+            }
+
+            build("assemble", options = buildOptions) {
+                assertSuccessful()
+            }
+        }
+    }
 }
diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/internal/kapt/KaptGenerateStubsTask.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/internal/kapt/KaptGenerateStubsTask.kt
index 9ea51cfcee0..989c990e7ce 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/internal/kapt/KaptGenerateStubsTask.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/internal/kapt/KaptGenerateStubsTask.kt
@@ -57,8 +57,8 @@ abstract class KaptGenerateStubsTask : KotlinCompile(KotlinJvmOptionsImpl()) {
                 providerFactory.provider {
                     kotlinCompileTask.getSourceRoots().let { compileTaskSourceRoots ->
                         SourceRoots.ForJvm(
-                            compileTaskSourceRoots.kotlinSourceFiles.filterTo(mutableListOf()) { task.isSourceRootAllowed(it) },
-                            javaSourceRootsProvider = { compileTaskSourceRoots.javaSourceRoots.filterTo(mutableSetOf()) { task.isSourceRootAllowed(it) } }
+                            compileTaskSourceRoots.kotlinSourceFiles.filter { task.isSourceRootAllowed(it) },
+                            compileTaskSourceRoots.javaSourceRoots.filter { task.isSourceRootAllowed(it) }
                         )
                     }
                 }
diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/tasks/KotlinCompileCommon.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/tasks/KotlinCompileCommon.kt
index 392d180b8c1..b0ae22e52bb 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/tasks/KotlinCompileCommon.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/tasks/KotlinCompileCommon.kt
@@ -127,6 +127,6 @@ abstract class KotlinCompileCommon @Inject constructor(
             reportingSettings = reportingSettings,
             outputFiles = allOutputFiles()
         )
-        compilerRunner.runMetadataCompilerAsync(sourceRoots.kotlinSourceFiles, args, environment)
+        compilerRunner.runMetadataCompilerAsync(sourceRoots.kotlinSourceFiles.files.toList(), args, environment)
     }
 }
diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/tasks/SourceRoots.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/tasks/SourceRoots.kt
index c22970c3463..59cf73033bb 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/tasks/SourceRoots.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/tasks/SourceRoots.kt
@@ -11,62 +11,58 @@ import org.jetbrains.kotlin.gradle.utils.isJavaFile
 import org.jetbrains.kotlin.gradle.utils.isKotlinFile
 import org.jetbrains.kotlin.gradle.utils.isParentOf
 import java.io.File
-import java.util.*
 import java.util.concurrent.Callable
 
-internal sealed class SourceRoots(val kotlinSourceFiles: List<File>) {
+internal sealed class SourceRoots(val kotlinSourceFiles: FileCollection) {
     private companion object {
         fun dumpPaths(files: Iterable<File>): String =
             "[${files.map { it.canonicalPath }.sorted().joinToString(prefix = "\n\t", separator = ",\n\t")}]"
     }
 
     open fun log(taskName: String, logger: Logger) {
-        logger.kotlinDebug { "$taskName source roots: ${dumpPaths(kotlinSourceFiles)}" }
+        logger.kotlinDebug { "$taskName source roots: ${dumpPaths(kotlinSourceFiles.files)}" }
     }
 
     class ForJvm constructor(
-        kotlinSourceFiles: List<File>,
-        private val javaSourceRootsProvider: () -> Set<File>
+        kotlinSourceFiles: FileCollection,
+        val javaSourceRoots: FileCollection
     ) : SourceRoots(kotlinSourceFiles) {
-        val javaSourceRoots: Set<File>
-            get() = javaSourceRootsProvider()
-
-        constructor(kotlinSourceFiles: List<File>, allSourceRoots: FileCollection, taskSource: FileCollection) : this(kotlinSourceFiles, {
-            findRootsForSources(allSourceRoots, taskSource.filter(File::isJavaFile)).toSet()
-        })
 
         companion object {
-            fun create(taskSource: FileTree, sourceRoots: FilteringSourceRootsContainer, sourceFilesExtensions: List<String>): ForJvm {
-                val kotlinSourceFiles = (taskSource as Iterable<File>).filter { it.isKotlinFile(sourceFilesExtensions) }
-                return ForJvm(kotlinSourceFiles, sourceRoots.sourceRoots, taskSource)
+            fun create(
+                taskSource: FileTree,
+                sourceRoots: FilteringSourceRootsContainer,
+                sourceFilesExtensions: List<String>
+            ): ForJvm {
+                return ForJvm(
+                    taskSource.filter { it.isKotlinFile(sourceFilesExtensions) },
+                    sourceRoots.sourceRoots.filterJavaRoots(
+                        taskSource.filter { it.isJavaFile() }
+                    )
+                )
             }
 
-            private fun findRootsForSources(allSourceRoots: Iterable<File>, sources: Iterable<File>): Set<File> {
-                val resultRoots = HashSet<File>()
-                val sourceDirs = sources.mapTo(HashSet()) { it.parentFile }
-
-                for (sourceDir in sourceDirs) {
-                    for (sourceRoot in allSourceRoots) {
-                        if (sourceRoot.isParentOf(sourceDir)) {
-                            resultRoots.add(sourceRoot)
-                        }
-                    }
-                }
-
-                return resultRoots
+            private fun FileCollection.filterJavaRoots(
+                sourceDirs: FileCollection
+            ): FileCollection = filter { sourceRoot ->
+                sourceDirs.asSequence().map { it.parentFile }.any { sourceRoot.isParentOf(it) }
             }
         }
 
         override fun log(taskName: String, logger: Logger) {
             super.log(taskName, logger)
-            logger.kotlinDebug { "$taskName java source roots: ${dumpPaths(javaSourceRoots)}" }
+            logger.kotlinDebug { "$taskName java source roots: ${dumpPaths(javaSourceRoots.files)}" }
         }
     }
 
-    class KotlinOnly(kotlinSourceFiles: List<File>) : SourceRoots(kotlinSourceFiles) {
+    class KotlinOnly(kotlinSourceFiles: FileCollection) : SourceRoots(kotlinSourceFiles) {
         companion object {
-            fun create(taskSource: FileTree, sourceFilesExtensions: List<String>) =
-                KotlinOnly((taskSource as Iterable<File>).filter { it.isKotlinFile(sourceFilesExtensions) })
+            fun create(
+                taskSource: FileTree,
+                sourceFilesExtensions: List<String>
+            ) = KotlinOnly(
+                taskSource.filter { it.isKotlinFile(sourceFilesExtensions) }
+            )
         }
     }
 }
diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/tasks/Tasks.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/tasks/Tasks.kt
index 4a199d24deb..dc37cf1bd15 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/tasks/Tasks.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/tasks/Tasks.kt
@@ -490,7 +490,7 @@ abstract class KotlinCompile @Inject constructor(
             kotlinScriptExtensions = sourceFilesExtensions.get().toTypedArray()
         )
         compilerRunner.runJvmCompilerAsync(
-            sourceRoots.kotlinSourceFiles,
+            sourceRoots.kotlinSourceFiles.files.toList(),
             commonSourceSet.toList(),
             sourceRoots.javaSourceRoots,
             javaPackagePrefix,
@@ -799,7 +799,12 @@ abstract class Kotlin2JsCompile @Inject constructor(
             reportingSettings = reportingSettings,
             incrementalCompilationEnvironment = icEnv
         )
-        compilerRunner.runJsCompilerAsync(sourceRoots.kotlinSourceFiles, commonSourceSet.toList(), args, environment)
+        compilerRunner.runJsCompilerAsync(
+            sourceRoots.kotlinSourceFiles.files.toList(),
+            commonSourceSet.toList(),
+            args,
+            environment
+        )
     }
 }