diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/MultiplatformGradleIT.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/MultiplatformGradleIT.kt
index ffbf759b6b2..43ecba62b8c 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/MultiplatformGradleIT.kt
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/MultiplatformGradleIT.kt
@@ -356,6 +356,9 @@ class MultiplatformGradleIT : BaseGradleIT() {
             options = defaultBuildOptions().copy(
                 androidGradlePluginVersion = AGPVersion.v4_2_0,
                 androidHome = KtTestUtil.findAndroidSdk().also { acceptAndroidSdkLicenses(it) },
+                // Workaround for a deprecation warning from AGP
+                // Relying on FileTrees for ignoring empty directories when using @SkipWhenEmpty has been deprecated.
+                warningMode = WarningMode.None,
             ),
         ) {
             assertSuccessful()
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/NewMultiplatformIT.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/NewMultiplatformIT.kt
index 689557e2c09..ca5af575c05 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/NewMultiplatformIT.kt
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/NewMultiplatformIT.kt
@@ -1626,7 +1626,12 @@ class NewMultiplatformIT : BaseGradleIT() {
         build(
             "assembleDebug",
             // https://issuetracker.google.com/issues/152187160
-            options = defaultBuildOptions().copy(androidGradlePluginVersion = AGPVersion.v4_2_0)
+            options = defaultBuildOptions().copy(
+                androidGradlePluginVersion = AGPVersion.v4_2_0,
+                // Workaround for a deprecation warning from AGP
+                // Relying on FileTrees for ignoring empty directories when using @SkipWhenEmpty has been deprecated.
+                warningMode = WarningMode.None,
+            )
         ) {
             assertSuccessful()
             assertNotContains(
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/android/ConfigurationCacheForAndroidIT.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/android/ConfigurationCacheForAndroidIT.kt
index 5dd20a77051..381f05b2970 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/android/ConfigurationCacheForAndroidIT.kt
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/android/ConfigurationCacheForAndroidIT.kt
@@ -5,6 +5,7 @@
 
 package org.jetbrains.kotlin.gradle.android
 
+import org.gradle.api.logging.configuration.WarningMode
 import org.gradle.util.GradleVersion
 import org.jetbrains.kotlin.gradle.AbstractConfigurationCacheIT
 import org.jetbrains.kotlin.gradle.testbase.*
@@ -15,7 +16,10 @@ import org.junit.jupiter.api.DisplayName
 @AndroidGradlePluginTests
 class ConfigurationCacheForAndroidIT : AbstractConfigurationCacheIT() {
     override val defaultBuildOptions = super.defaultBuildOptions.copy(
-        androidVersion = AGP_42
+        androidVersion = AGP_42,
+        // Workaround for a deprecation warning from AGP
+        // Relying on FileTrees for ignoring empty directories when using @SkipWhenEmpty has been deprecated.
+        warningMode = WarningMode.None,
     )
 
     @DisplayName("works in android plus kapt project")
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/android/KotlinAndroidMppIT.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/android/KotlinAndroidMppIT.kt
index 67db9bcf546..c21def38ff1 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/android/KotlinAndroidMppIT.kt
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/android/KotlinAndroidMppIT.kt
@@ -5,6 +5,7 @@
 
 package org.jetbrains.kotlin.gradle.android
 
+import org.gradle.api.logging.configuration.WarningMode
 import org.gradle.util.GradleVersion
 import org.jetbrains.kotlin.gradle.testbase.*
 import org.jetbrains.kotlin.gradle.tooling.BuildKotlinToolingMetadataTask
@@ -833,7 +834,12 @@ class KotlinAndroidMppIT : KGPBaseTest() {
 
             checkedConsumerAGPVersions.forEach { consumerAgpVersion ->
                 println("Testing compatibility for AGP consumer version $consumerAgpVersion (Producer: $agpVersion)")
-                val buildOptions = buildOptions.copy(androidVersion = consumerAgpVersion)
+                val buildOptions = buildOptions.copy(
+                    androidVersion = consumerAgpVersion,
+                    // Workaround for a deprecation warning from AGP
+                    // Relying on FileTrees for ignoring empty directories when using @SkipWhenEmpty has been deprecated.
+                    warningMode = if (AGPVersion.fromString(consumerAgpVersion) <= AGPVersion.v7_1_0) WarningMode.None else WarningMode.Fail,
+                )
 
                 /*
                 Project: multiplatformAndroidConsumer is a mpp project with jvm and android targets.
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/android/MultiplatformAndroidSourceSetLayoutV2IT.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/android/MultiplatformAndroidSourceSetLayoutV2IT.kt
index c13ae4b6c83..c39fbad9627 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/android/MultiplatformAndroidSourceSetLayoutV2IT.kt
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/android/MultiplatformAndroidSourceSetLayoutV2IT.kt
@@ -5,8 +5,10 @@
 
 package org.jetbrains.kotlin.gradle.android
 
+import org.gradle.api.logging.configuration.WarningMode
 import org.gradle.util.GradleVersion
 import org.jetbrains.kotlin.gradle.testbase.*
+import org.jetbrains.kotlin.gradle.util.AGPVersion
 import org.junit.jupiter.api.DisplayName
 import kotlin.test.assertNull
 
@@ -21,7 +23,12 @@ class MultiplatformAndroidSourceSetLayoutV2IT : KGPBaseTest() {
         project(
             "multiplatformAndroidSourceSetLayout2",
             gradleVersion,
-            defaultBuildOptions.copy(androidVersion = agpVersion),
+            defaultBuildOptions.copy(
+                androidVersion = agpVersion,
+                // Workaround for a deprecation warning from AGP
+                // Relying on FileTrees for ignoring empty directories when using @SkipWhenEmpty has been deprecated.
+                warningMode = if (AGPVersion.fromString(agpVersion) <= AGPVersion.v7_1_0) WarningMode.None else WarningMode.Fail,
+            ),
             buildJdk = jdkVersion.location
         ) {
             build("test") {
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/mpp/AndroidAndJavaConsumeMppLibIT.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/mpp/AndroidAndJavaConsumeMppLibIT.kt
index 49d68b55041..eba2d747fac 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/mpp/AndroidAndJavaConsumeMppLibIT.kt
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/mpp/AndroidAndJavaConsumeMppLibIT.kt
@@ -6,6 +6,7 @@
 
 package org.jetbrains.kotlin.gradle.mpp
 
+import org.gradle.api.logging.configuration.WarningMode
 import org.jetbrains.kotlin.gradle.BaseGradleIT
 import org.jetbrains.kotlin.gradle.GradleVersionRequired
 import org.jetbrains.kotlin.gradle.embedProject
@@ -122,7 +123,10 @@ abstract class AndroidAndJavaConsumeMppLibIT : BaseGradleIT() {
         val producerBuildOptions = defaultBuildOptions().copy(
             javaHome = jdk11Home,
             androidHome = KtTestUtil.findAndroidSdk(),
-            androidGradlePluginVersion = producerAgpVersion
+            androidGradlePluginVersion = producerAgpVersion,
+            // Workaround for a deprecation warning from AGP
+            // Relying on FileTrees for ignoring empty directories when using @SkipWhenEmpty has been deprecated.
+            warningMode = if (producerAgpVersion <= AGPVersion.v7_1_0) WarningMode.None else WarningMode.Fail,
         )
         producerBuildOptions.androidHome?.let { acceptAndroidSdkLicenses(it) }