diff --git a/atomicfu-gradle-plugin/src/main/kotlin/kotlinx/atomicfu/plugin/gradle/AtomicFUGradlePlugin.kt b/atomicfu-gradle-plugin/src/main/kotlin/kotlinx/atomicfu/plugin/gradle/AtomicFUGradlePlugin.kt
index bb9a521d..212f0a6e 100644
--- a/atomicfu-gradle-plugin/src/main/kotlin/kotlinx/atomicfu/plugin/gradle/AtomicFUGradlePlugin.kt
+++ b/atomicfu-gradle-plugin/src/main/kotlin/kotlinx/atomicfu/plugin/gradle/AtomicFUGradlePlugin.kt
@@ -74,8 +74,8 @@ private fun Project.checkCompatibility(afuPluginVersion: String) {
         )
     }
     if (!kotlinVersion.atLeast(1, 9, 0)) {
-        // Since Kotlin 1.9.0 the logic of the Gradle plugin from the Kotlin repo (AtomicfuKotlinGradleSubplugin) 
-        // may be moved to the Gradle plugin in the library. The sources of the compiler plugin 
+        // Since Kotlin 1.9.0 the logic of the Gradle plugin from the Kotlin repo (AtomicfuKotlinGradleSubplugin)
+        // may be moved to the Gradle plugin in the library. The sources of the compiler plugin
         // are published as `kotlin-atomicfu-compiler-plugin-embeddable` since Kotlin 1.9.0 and may be accessed out of the Kotlin repo.
         error(
             "You are applying `kotlinx-atomicfu` plugin of version $afuPluginVersion. " +
@@ -487,6 +487,7 @@ abstract class AtomicFUTransformTask : ConventionTask() {
 
     @TaskAction
     fun transform() {
+        destinationDirectory.get().asFile.deleteRecursively()
         val cp = classPath.files.map { it.absolutePath }
         inputFiles.files.forEach { inputDir ->
             AtomicFUTransformer(cp, inputDir, destinationDirectory.get().asFile).let { t ->
diff --git a/integration-testing/src/functionalTest/kotlin/kotlinx.atomicfu.gradle.plugin.test/cases/JvmProjectTest.kt b/integration-testing/src/functionalTest/kotlin/kotlinx.atomicfu.gradle.plugin.test/cases/JvmProjectTest.kt
index de673131..14256794 100644
--- a/integration-testing/src/functionalTest/kotlin/kotlinx.atomicfu.gradle.plugin.test/cases/JvmProjectTest.kt
+++ b/integration-testing/src/functionalTest/kotlin/kotlinx.atomicfu.gradle.plugin.test/cases/JvmProjectTest.kt
@@ -33,10 +33,50 @@ class JvmProjectTest {
         jvmSample.checkConsumableDependencies(false)
         jvmSample.buildAndCheckBytecode()
     }
-    
+
     // This test checks that jar is packed without duplicates, see #303
     @Test
     fun testJar() {
         assertTrue(jvmSample.cleanAndJar().isSuccessful)
     }
+
+    @Test
+    fun testFilesDeleted() {
+
+        val buildClassesAtomicfuDir = jvmSample.targetDir.resolve("build/classes/atomicfu")
+
+        /** Get all that Atomicfu generates in `build/classes/atomicfu/` */
+        fun buildClassesAtomicFuDirFiles(): String =
+            buildClassesAtomicfuDir.walk()
+                .filter { it.isFile }
+                .map { it.relativeTo(jvmSample.targetDir).invariantSeparatorsPath }
+                .sorted()
+                .joinToString("\n")
+
+        jvmSample.build().apply {
+            assertTrue { buildClassesAtomicfuDir.exists() }
+            assertEquals(
+                """
+                build/classes/atomicfu/main/IntArithmetic.class
+                build/classes/atomicfu/main/META-INF/jvm-sample.kotlin_module
+                build/classes/atomicfu/main/MainKt.class
+                build/classes/atomicfu/test/ArithmeticTest.class
+                build/classes/atomicfu/test/META-INF/jvm-sample_test.kotlin_module
+                """.trimIndent(),
+                buildClassesAtomicFuDirFiles()
+            )
+        }
+
+        val projectSrcDir = jvmSample.targetDir.resolve("src")
+        projectSrcDir.deleteRecursively()
+        assertFalse { projectSrcDir.exists() }
+
+        jvmSample.build().apply {
+            assertTrue { buildClassesAtomicfuDir.exists() }
+            assertEquals(
+                "",
+                buildClassesAtomicFuDirFiles(),
+            )
+        }
+    }
 }
diff --git a/integration-testing/src/functionalTest/kotlin/kotlinx.atomicfu.gradle.plugin.test/framework/runner/BuildRunner.kt b/integration-testing/src/functionalTest/kotlin/kotlinx.atomicfu.gradle.plugin.test/framework/runner/BuildRunner.kt
index 867c0d39..8add7254 100644
--- a/integration-testing/src/functionalTest/kotlin/kotlinx.atomicfu.gradle.plugin.test/framework/runner/BuildRunner.kt
+++ b/integration-testing/src/functionalTest/kotlin/kotlinx.atomicfu.gradle.plugin.test/framework/runner/BuildRunner.kt
@@ -7,6 +7,9 @@ package kotlinx.atomicfu.gradle.plugin.test.framework.runner
 import java.io.File
 import java.nio.file.Files
 
+/**
+ * @param[targetDir] The root Gradle project directory.
+ */
 internal class GradleBuild(val projectName: String, val targetDir: File) {
     var enableJvmIrTransformation = false
     var enableJsIrTransformation = false
diff --git a/integration-testing/src/functionalTest/kotlin/kotlinx.atomicfu.gradle.plugin.test/framework/runner/Commands.kt b/integration-testing/src/functionalTest/kotlin/kotlinx.atomicfu.gradle.plugin.test/framework/runner/Commands.kt
index 13d1fec4..a895cab3 100644
--- a/integration-testing/src/functionalTest/kotlin/kotlinx.atomicfu.gradle.plugin.test/framework/runner/Commands.kt
+++ b/integration-testing/src/functionalTest/kotlin/kotlinx.atomicfu.gradle.plugin.test/framework/runner/Commands.kt
@@ -6,6 +6,11 @@ package kotlinx.atomicfu.gradle.plugin.test.framework.runner
 
 import kotlinx.atomicfu.gradle.plugin.test.framework.checker.getProjectClasspath
 
+internal fun GradleBuild.build(): BuildResult =
+    runGradle(listOf("build")).also {
+        require(it.isSuccessful) { "${this.projectName}:build task FAILED: ${it.output} " }
+    }
+
 internal fun GradleBuild.cleanAndBuild(): BuildResult =
     runGradle(listOf("clean", "build")).also {
         require(it.isSuccessful) { "${this.projectName}:build task FAILED: ${it.output} " }
@@ -13,8 +18,8 @@ internal fun GradleBuild.cleanAndBuild(): BuildResult =
 
 internal fun GradleBuild.cleanAndJar(): BuildResult = runGradle(listOf("clean", "jar"))
 
-internal fun GradleBuild.dependencies(): BuildResult = 
-    runGradle(listOf("dependencies")).also { 
+internal fun GradleBuild.dependencies(): BuildResult =
+    runGradle(listOf("dependencies")).also {
         require(it.isSuccessful) { "${this.projectName}:dependencies task FAILED: ${it.output} " }
     }