diff --git a/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/main/java/org/springframework/boot/gradle/tasks/bundling/BootJar.java b/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/main/java/org/springframework/boot/gradle/tasks/bundling/BootJar.java
index 37971ba11bb1..c53e42f40059 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/main/java/org/springframework/boot/gradle/tasks/bundling/BootJar.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/main/java/org/springframework/boot/gradle/tasks/bundling/BootJar.java
@@ -27,10 +27,12 @@
 import org.gradle.api.file.FileCopyDetails;
 import org.gradle.api.file.FileTreeElement;
 import org.gradle.api.internal.file.copy.CopyAction;
+import org.gradle.api.plugins.JavaPluginConvention;
 import org.gradle.api.specs.Spec;
 import org.gradle.api.tasks.Internal;
 import org.gradle.api.tasks.Nested;
 import org.gradle.api.tasks.Optional;
+import org.gradle.api.tasks.SourceSet;
 import org.gradle.api.tasks.bundling.Jar;
 
 /**
@@ -103,7 +105,12 @@ public void copy() {
 	@Override
 	protected CopyAction createCopyAction() {
 		if (this.layered != null) {
-			LayerResolver layerResolver = new LayerResolver(getConfigurations(), this.layered, this::isLibrary);
+			JavaPluginConvention javaPluginConvention = getProject().getConvention()
+					.findPlugin(JavaPluginConvention.class);
+			Iterable<SourceSet> sourceSets = (javaPluginConvention != null) ? javaPluginConvention.getSourceSets()
+					: Collections.emptySet();
+			LayerResolver layerResolver = new LayerResolver(sourceSets, getConfigurations(), this.layered,
+					this::isLibrary);
 			String layerToolsLocation = this.layered.isIncludeLayerTools() ? LIB_DIRECTORY : null;
 			return this.support.createCopyAction(this, layerResolver, layerToolsLocation);
 		}
diff --git a/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/main/java/org/springframework/boot/gradle/tasks/bundling/LayerResolver.java b/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/main/java/org/springframework/boot/gradle/tasks/bundling/LayerResolver.java
index 2fc47fd68200..bbeee6d6e44a 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/main/java/org/springframework/boot/gradle/tasks/bundling/LayerResolver.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/main/java/org/springframework/boot/gradle/tasks/bundling/LayerResolver.java
@@ -17,8 +17,6 @@
 package org.springframework.boot.gradle.tasks.bundling;
 
 import java.io.File;
-import java.util.Arrays;
-import java.util.Collections;
 import java.util.HashSet;
 import java.util.LinkedHashMap;
 import java.util.Map;
@@ -30,6 +28,7 @@
 import org.gradle.api.artifacts.ResolvedConfiguration;
 import org.gradle.api.file.FileCopyDetails;
 import org.gradle.api.specs.Spec;
+import org.gradle.api.tasks.SourceSet;
 
 import org.springframework.boot.loader.tools.Layer;
 import org.springframework.boot.loader.tools.Library;
@@ -53,9 +52,9 @@ class LayerResolver {
 
 	private final Spec<FileCopyDetails> librarySpec;
 
-	LayerResolver(Iterable<Configuration> configurations, LayeredSpec layeredConfiguration,
-			Spec<FileCopyDetails> librarySpec) {
-		this.resolvedDependencies = new ResolvedDependencies(configurations);
+	LayerResolver(Iterable<SourceSet> sourceSets, Iterable<Configuration> configurations,
+			LayeredSpec layeredConfiguration, Spec<FileCopyDetails> librarySpec) {
+		this.resolvedDependencies = new ResolvedDependencies(sourceSets, configurations);
 		this.layeredConfiguration = layeredConfiguration;
 		this.librarySpec = librarySpec;
 	}
@@ -96,19 +95,41 @@ private Library asLibrary(FileCopyDetails details) {
 	 */
 	private static class ResolvedDependencies {
 
-		private static final Set<String> DEPRECATED_FOR_RESOLUTION_CONFIGURATIONS = Collections
-				.unmodifiableSet(new HashSet<>(Arrays.asList("archives", "compile", "compileOnly", "default", "runtime",
-						"testCompile", "testCompileOnly", "testRuntime")));
+		private final Set<String> deprecatedForResolutionConfigurationNames;
 
 		private final Map<Configuration, ResolvedConfigurationDependencies> configurationDependencies = new LinkedHashMap<>();
 
-		ResolvedDependencies(Iterable<Configuration> configurations) {
+		ResolvedDependencies(Iterable<SourceSet> sourceSets, Iterable<Configuration> configurations) {
+			this.deprecatedForResolutionConfigurationNames = deprecatedForResolutionConfigurationNames(sourceSets);
 			configurations.forEach(this::processConfiguration);
 		}
 
+		@SuppressWarnings("deprecation")
+		private Set<String> deprecatedForResolutionConfigurationNames(Iterable<SourceSet> sourceSets) {
+			Set<String> configurationNames = new HashSet<>();
+			configurationNames.add("archives");
+			configurationNames.add("default");
+			for (SourceSet sourceSet : sourceSets) {
+				try {
+					configurationNames.add(sourceSet.getCompileConfigurationName());
+				}
+				catch (NoSuchMethodError ex) {
+					// Continue
+				}
+				configurationNames.add(sourceSet.getCompileOnlyConfigurationName());
+				try {
+					configurationNames.add(sourceSet.getRuntimeConfigurationName());
+				}
+				catch (NoSuchMethodError ex) {
+					// Continue
+				}
+			}
+			return configurationNames;
+		}
+
 		private void processConfiguration(Configuration configuration) {
 			if (configuration.isCanBeResolved()
-					&& !DEPRECATED_FOR_RESOLUTION_CONFIGURATIONS.contains(configuration.getName())) {
+					&& !this.deprecatedForResolutionConfigurationNames.contains(configuration.getName())) {
 				this.configurationDependencies.put(configuration,
 						new ResolvedConfigurationDependencies(configuration.getResolvedConfiguration()));
 			}
diff --git a/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/test/java/org/springframework/boot/gradle/tasks/bundling/BootJarIntegrationTests.java b/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/test/java/org/springframework/boot/gradle/tasks/bundling/BootJarIntegrationTests.java
index a3f7459bddb3..ada979dd2f56 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/test/java/org/springframework/boot/gradle/tasks/bundling/BootJarIntegrationTests.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/test/java/org/springframework/boot/gradle/tasks/bundling/BootJarIntegrationTests.java
@@ -86,6 +86,11 @@ void notUpToDateWhenBuiltWithLayersAndToolsAndThenWithLayersAndWithoutTools()
 				.getOutcome()).isEqualTo(TaskOutcome.SUCCESS);
 	}
 
+	@TestTemplate
+	void layersWithCustomSourceSet() throws IOException {
+		assertThat(this.gradleBuild.build("bootJar").task(":bootJar").getOutcome()).isEqualTo(TaskOutcome.SUCCESS);
+	}
+
 	@TestTemplate
 	void implicitLayers() throws IOException {
 		writeMainClass();
diff --git a/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/test/resources/org/springframework/boot/gradle/tasks/bundling/BootJarIntegrationTests-layersWithCustomSourceSet.gradle b/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/test/resources/org/springframework/boot/gradle/tasks/bundling/BootJarIntegrationTests-layersWithCustomSourceSet.gradle
new file mode 100644
index 000000000000..2cbb899f1c5c
--- /dev/null
+++ b/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/test/resources/org/springframework/boot/gradle/tasks/bundling/BootJarIntegrationTests-layersWithCustomSourceSet.gradle
@@ -0,0 +1,36 @@
+plugins {
+	id 'java'
+	id 'org.springframework.boot' version '{version}'
+}
+
+sourceSets {
+	custom
+}
+
+bootJar {
+	mainClassName = 'com.example.Application'
+	layered()
+}
+
+repositories {
+	mavenCentral()
+	maven { url "file:repository" }
+}
+
+dependencies {
+	implementation("com.example:library:1.0-SNAPSHOT")
+	implementation("org.apache.commons:commons-lang3:3.9")
+	implementation("org.springframework:spring-core:5.2.5.RELEASE")
+}
+
+task listLayers(type: JavaExec) {
+	classpath = bootJar.outputs.files
+	systemProperties = [ "jarmode": "layertools" ]
+	args "list"
+}
+
+task extractLayers(type: JavaExec) {
+	classpath = bootJar.outputs.files
+	systemProperties = [ "jarmode": "layertools" ]
+	args "extract"
+}