diff --git a/CHANGELOG.md b/CHANGELOG.md
index 843f63901..4a1699c1c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@ We use [semantic versioning](http://semver.org/):
 - [fix] _agent_, _teamscale-gradle-plugin_, _teamscale-maven-plugin_: A corrupt class file whose class name cannot be read is skipped with a warning instead of failing the coverage report.
 - [fix] _impacted-test-engine_: A test that a failing assumption aborts is reported as skipped instead of as an error.
 - [fix] _teamscale-gradle-plugin_: The plugin now works when the build sets `jacoco.excludes` or the JUnit Platform `excludeEngines` of a test task to a read-only collection (for example, `listOf(...)` or `setOf(...)` in the Kotlin DSL). Previously, applying the plugin or running the test task failed with an `UnsupportedOperationException`.
+- [fix] _teamscale-gradle-plugin_: Applying `com.teamscale.aggregation` no longer emits deprecation warnings on Gradle 9.6 and newer.
 - [fix] _teamscale-gradle-plugin_: The default excludes now match Mockito mocks (e.g. `com.company.IFoo$MockitoMock$123`) and Guice fast classes (e.g. `com.company.Foo$$FastClassByGuice$$abc`). Previously the profiler instrumented them, and the testwise coverage report warned that it found coverage for classes that were not provided.
 
 # 39.0.0
diff --git a/system-tests/gradle-multi-module/gradle-project/gradle.properties b/system-tests/gradle-multi-module/gradle-project/gradle.properties
index e8a5b0e32..2e17348d8 100644
--- a/system-tests/gradle-multi-module/gradle-project/gradle.properties
+++ b/system-tests/gradle-multi-module/gradle-project/gradle.properties
@@ -2,3 +2,4 @@ org.gradle.configuration-cache=true
 org.gradle.configuration-cache.problems=FAIL
 org.gradle.configuration-cache.parallel=true
 org.gradle.daemon=false
+org.gradle.isolated-projects=true
diff --git a/system-tests/gradle-multi-module/src/test/kotlin/com/teamscale/tia/IsolatedProjectsTest.kt b/system-tests/gradle-multi-module/src/test/kotlin/com/teamscale/tia/IsolatedProjectsTest.kt
new file mode 100644
index 000000000..73a537078
--- /dev/null
+++ b/system-tests/gradle-multi-module/src/test/kotlin/com/teamscale/tia/IsolatedProjectsTest.kt
@@ -0,0 +1,22 @@
+package com.teamscale.tia
+
+import com.teamscale.test.commons.SystemTestUtils.runGradle
+import org.assertj.core.api.Assertions.assertThat
+import org.junit.jupiter.api.Test
+
+/**
+ * Checks that the plugins are compatible with [Isolated Projects](https://docs.gradle.org/current/userguide/isolated_projects.html).
+ * It is enabled via gradle.properties, so every build of the test project fails on a violation.
+ */
+class IsolatedProjectsTest {
+	@Test
+	fun testIsolatedProjects() {
+		val result = runGradle(
+			"gradle-project", "clean",
+			"unitTestAggregateCompactCoverageReport", "unitTestAggregateJUnitReport",
+			"systemTestAggregateTestwiseCoverageReport"
+		)
+		// Guards against the tests of this module silently running without Isolated Projects.
+		assertThat(result.stdout).contains("Isolated Projects is an incubating feature")
+	}
+}
diff --git a/teamscale-gradle-plugin/build.gradle.kts b/teamscale-gradle-plugin/build.gradle.kts
index 00981093d..2185412e5 100644
--- a/teamscale-gradle-plugin/build.gradle.kts
+++ b/teamscale-gradle-plugin/build.gradle.kts
@@ -42,6 +42,7 @@ gradlePlugin {
 			compatibility {
 				features {
 					configurationCache = true
+					isolatedProjects = true
 				}
 			}
 		}
@@ -54,6 +55,7 @@ gradlePlugin {
 			compatibility {
 				features {
 					configurationCache = true
+					isolatedProjects = true
 				}
 			}
 		}
diff --git a/teamscale-gradle-plugin/src/main/kotlin/com/teamscale/aggregation/ReportAggregationPlugin.kt b/teamscale-gradle-plugin/src/main/kotlin/com/teamscale/aggregation/ReportAggregationPlugin.kt
index b0ba46a8e..18021669c 100755
--- a/teamscale-gradle-plugin/src/main/kotlin/com/teamscale/aggregation/ReportAggregationPlugin.kt
+++ b/teamscale-gradle-plugin/src/main/kotlin/com/teamscale/aggregation/ReportAggregationPlugin.kt
@@ -48,24 +48,22 @@ abstract class ReportAggregationPlugin : Plugin<Project> {
 	@get:Inject
 	protected abstract val jvmPluginServices: JvmPluginServices
 
-	@Suppress("DEPRECATION")
 	override fun apply(project: Project) {
 		val configurations = project.configurations
 		val reportAggregation =
 			configurations.dependencyScope(REPORT_AGGREGATION_CONFIGURATION_NAME) {
 				description = "A configuration to collect reports across projects."
-				isVisible = false
 			}.get()
 
 		val aggregateReportResults = configurations.resolvable(AGGREGATE_REPORT_RESULTS_CONFIGURATION_NAME) {
 			extendsFrom(reportAggregation)
 			description =
 				"Resolvable configuration used to gather files for report aggregation via ArtifactViews, not intended to be used directly"
-			isVisible = false
 		}.get()
 
 		project.plugins.withType<JavaBasePlugin> {
-			reportAggregation.dependencies.add(project.dependencyFactory.create(project))
+			// The map notation is the only way to create a project dependency that works on Gradle 8 and is not deprecated on Gradle 9.
+			reportAggregation.dependencies.add(project.dependencies.project(mapOf("path" to project.path)))
 			// If the current project is jvm-based, aggregate dependent projects as jvm-based as well.
 			jvmPluginServices.configureAsRuntimeElements(aggregateReportResults)
 		}
diff --git a/teamscale-gradle-plugin/src/test/kotlin/com/teamscale/DeprecationWarningTest.kt b/teamscale-gradle-plugin/src/test/kotlin/com/teamscale/DeprecationWarningTest.kt
new file mode 100644
index 000000000..a7c1fb3db
--- /dev/null
+++ b/teamscale-gradle-plugin/src/test/kotlin/com/teamscale/DeprecationWarningTest.kt
@@ -0,0 +1,46 @@
+package com.teamscale
+
+import org.junit.jupiter.api.BeforeEach
+import org.junit.jupiter.api.Test
+
+/**
+ * Tests that applying the plugins emits no deprecation warnings. Runs on the Gradle version that builds the plugin,
+ * since new deprecations only show up on newer Gradle versions than the minimum supported one.
+ */
+class DeprecationWarningTest : TeamscalePluginTestBase() {
+
+	override val gradleVersion: String? = null
+
+	@BeforeEach
+	fun init() {
+		rootProject.settingsFile.writeText("rootProject.name = 'deprecations'")
+	}
+
+	@Test
+	fun `aggregation plugin emits no deprecation warning`() {
+		rootProject.buildFile.writeText(
+			"""
+plugins {
+	id 'com.teamscale.aggregation'
+}
+			""".trimIndent()
+		)
+
+		run("help", "--warning-mode=fail")
+	}
+
+	@Test
+	fun `aggregation plugin in a Java project emits no deprecation warning`() {
+		rootProject.buildFile.writeText(
+			"""
+plugins {
+	id 'java'
+	id 'com.teamscale'
+	id 'com.teamscale.aggregation'
+}
+			""".trimIndent()
+		)
+
+		run("help", "--warning-mode=fail")
+	}
+}
diff --git a/teamscale-gradle-plugin/src/test/kotlin/com/teamscale/TeamscalePluginTestBase.kt b/teamscale-gradle-plugin/src/test/kotlin/com/teamscale/TeamscalePluginTestBase.kt
index 41e9a7e12..667946cbf 100644
--- a/teamscale-gradle-plugin/src/test/kotlin/com/teamscale/TeamscalePluginTestBase.kt
+++ b/teamscale-gradle-plugin/src/test/kotlin/com/teamscale/TeamscalePluginTestBase.kt
@@ -31,6 +31,9 @@ abstract class TeamscalePluginTestBase {
 			System.getProperty("systemTestCoverageAgent")?.takeIf { it.none(Char::isWhitespace) }
 	}
 
+	/** The Gradle version to run the builds with, or null for the Gradle distribution that runs the tests. */
+	protected open val gradleVersion: String? = TeamscalePlugin.MINIMUM_SUPPORTED_VERSION.version
+
 	/** Teamscale mock server to be used during the tests. */
 	protected lateinit var teamscaleMockServer: TeamscaleMockServer
 
@@ -87,7 +90,7 @@ abstract class TeamscalePluginTestBase {
 			.withProjectDir(rootProject.projectDir)
 			.withPluginClasspath()
 			.withArguments(runnerArgs)
-			.withGradleVersion(TeamscalePlugin.MINIMUM_SUPPORTED_VERSION.version)
+		gradleVersion?.let { runner.withGradleVersion(it) }
 
 		return runner
 	}