diff --git a/initializr-generator-spring/src/test/resources/project/gradle/annotation-processor-dependency-build.gradle.kts.gen b/initializr-generator-spring/src/test/resources/project/gradle/annotation-processor-dependency-build.gradle.kts.gen
index 63d69d1c..6ade62aa 100644
--- a/initializr-generator-spring/src/test/resources/project/gradle/annotation-processor-dependency-build.gradle.kts.gen
+++ b/initializr-generator-spring/src/test/resources/project/gradle/annotation-processor-dependency-build.gradle.kts.gen
@@ -10,7 +10,7 @@ java.sourceCompatibility = JavaVersion.VERSION_1_8
 
 configurations {
 	compileOnly {
-		extendsFrom(annotationProcessor)
+		extendsFrom(configurations.annotationProcessor.get())
 	}
 }
 
diff --git a/initializr-generator/src/main/java/io/spring/initializr/generator/buildsystem/gradle/GradleBuildWriter.java b/initializr-generator/src/main/java/io/spring/initializr/generator/buildsystem/gradle/GradleBuildWriter.java
index 61e38964..eb17690e 100644
--- a/initializr-generator/src/main/java/io/spring/initializr/generator/buildsystem/gradle/GradleBuildWriter.java
+++ b/initializr-generator/src/main/java/io/spring/initializr/generator/buildsystem/gradle/GradleBuildWriter.java
@@ -86,7 +86,7 @@ public abstract class GradleBuildWriter {
 	protected abstract void writeConfigurations(IndentingWriter writer, GradleBuild build);
 
 	protected abstract void writeConfiguration(IndentingWriter writer, String configurationName,
-			ConfigurationCustomization configurationCustomization);
+			ConfigurationCustomization configurationCustomization, List<String> customConfigurations);
 
 	protected final void writeRepositories(IndentingWriter writer, GradleBuild build) {
 		writeNestedCollection(writer, "repositories", build.repositories().items().collect(Collectors.toList()),
diff --git a/initializr-generator/src/main/java/io/spring/initializr/generator/buildsystem/gradle/GroovyDslGradleBuildWriter.java b/initializr-generator/src/main/java/io/spring/initializr/generator/buildsystem/gradle/GroovyDslGradleBuildWriter.java
index ed0efc8f..2dad6036 100644
--- a/initializr-generator/src/main/java/io/spring/initializr/generator/buildsystem/gradle/GroovyDslGradleBuildWriter.java
+++ b/initializr-generator/src/main/java/io/spring/initializr/generator/buildsystem/gradle/GroovyDslGradleBuildWriter.java
@@ -89,7 +89,7 @@ public class GroovyDslGradleBuildWriter extends GradleBuildWriter {
 
 	@Override
 	protected void writeConfiguration(IndentingWriter writer, String configurationName,
-			GradleBuild.ConfigurationCustomization configurationCustomization) {
+			GradleBuild.ConfigurationCustomization configurationCustomization, List<String> customConfigurations) {
 		writer.println(configurationName + " {");
 		writer.indented(() -> writer.println(
 				String.format("extendsFrom %s", String.join(", ", configurationCustomization.getExtendsFrom()))));
@@ -125,7 +125,7 @@ public class GroovyDslGradleBuildWriter extends GradleBuildWriter {
 		writer.indented(() -> {
 			configurations.forEach(writer::println);
 			configurationCustomizations
-					.forEach((name, customization) -> writeConfiguration(writer, name, customization));
+					.forEach((name, customization) -> writeConfiguration(writer, name, customization, configurations));
 		});
 		writer.println("}");
 		writer.println("");
diff --git a/initializr-generator/src/main/java/io/spring/initializr/generator/buildsystem/gradle/KotlinDslGradleBuildWriter.java b/initializr-generator/src/main/java/io/spring/initializr/generator/buildsystem/gradle/KotlinDslGradleBuildWriter.java
index 6155156d..cc502b9a 100644
--- a/initializr-generator/src/main/java/io/spring/initializr/generator/buildsystem/gradle/KotlinDslGradleBuildWriter.java
+++ b/initializr-generator/src/main/java/io/spring/initializr/generator/buildsystem/gradle/KotlinDslGradleBuildWriter.java
@@ -16,8 +16,10 @@
 
 package io.spring.initializr.generator.buildsystem.gradle;
 
+import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
 
@@ -104,18 +106,27 @@ public class KotlinDslGradleBuildWriter extends GradleBuildWriter {
 
 	@Override
 	protected void writeConfiguration(IndentingWriter writer, String configurationName,
-			ConfigurationCustomization configurationCustomization) {
+			ConfigurationCustomization configurationCustomization, List<String> customConfigurations) {
 		if (configurationCustomization.getExtendsFrom().isEmpty()) {
 			writer.println(configurationName);
 		}
 		else {
 			writer.println(configurationName + " {");
 			writer.indented(() -> writer.println(String.format("extendsFrom(%s)",
-					configurationCustomization.getExtendsFrom().stream().collect(Collectors.joining(", ")))));
+					configurationCustomization.getExtendsFrom().stream()
+							.map((name) -> configurationReference(name, customConfigurations))
+							.collect(Collectors.joining(", ")))));
 			writer.println("}");
 		}
 	}
 
+	private String configurationReference(String configurationName, Collection<String> customConfigurations) {
+		if (customConfigurations.contains(configurationName)) {
+			return configurationName;
+		}
+		return "configurations." + configurationName + ".get()";
+	}
+
 	@Override
 	protected String repositoryAsString(MavenRepository repository) {
 		if (MavenRepository.MAVEN_CENTRAL.equals(repository)) {
@@ -127,7 +138,8 @@ public class KotlinDslGradleBuildWriter extends GradleBuildWriter {
 	@Override
 	protected void writeConfigurations(IndentingWriter writer, GradleBuild build) {
 		Map<String, ConfigurationCustomization> configurationCustomizations = build.getConfigurationCustomizations();
-		for (String configuration : build.getConfigurations()) {
+		List<String> configurations = build.getConfigurations();
+		for (String configuration : configurations) {
 			writer.println("val " + configuration + " by configurations.creating");
 		}
 		if (configurationCustomizations.isEmpty()) {
@@ -135,7 +147,7 @@ public class KotlinDslGradleBuildWriter extends GradleBuildWriter {
 		}
 		writer.println("configurations {");
 		writer.indented(() -> configurationCustomizations
-				.forEach((name, customization) -> writeConfiguration(writer, name, customization)));
+				.forEach((name, customization) -> writeConfiguration(writer, name, customization, configurations)));
 		writer.println("}");
 		writer.println("");
 	}
diff --git a/initializr-generator/src/test/java/io/spring/initializr/generator/buildsystem/gradle/KotlinDslGradleBuildWriterTests.java b/initializr-generator/src/test/java/io/spring/initializr/generator/buildsystem/gradle/KotlinDslGradleBuildWriterTests.java
index 375c7745..c36f9e7b 100644
--- a/initializr-generator/src/test/java/io/spring/initializr/generator/buildsystem/gradle/KotlinDslGradleBuildWriterTests.java
+++ b/initializr-generator/src/test/java/io/spring/initializr/generator/buildsystem/gradle/KotlinDslGradleBuildWriterTests.java
@@ -277,21 +277,24 @@ class KotlinDslGradleBuildWriterTests {
 	@Test
 	void gradleBuildWithConfigurationCustomization() throws Exception {
 		GradleBuild build = new GradleBuild();
-		build.customizeConfiguration("runtimeClasspath", (configuration) -> configuration.extendsFrom("custom1"));
-		build.customizeConfiguration("runtimeClasspath", (configuration) -> configuration.extendsFrom("custom2"));
+		build.addConfiguration("custom");
+		build.customizeConfiguration("runtimeClasspath", (configuration) -> configuration.extendsFrom("custom"));
+		build.customizeConfiguration("runtimeClasspath", (configuration) -> configuration.extendsFrom("builtIn"));
 		List<String> lines = generateBuild(build);
-		assertThat(lines).containsSequence("configurations {", "    runtimeClasspath {",
-				"        extendsFrom(custom1, custom2)", "    }", "}");
+		assertThat(lines).containsSequence("val custom by configurations.creating", "configurations {",
+				"    runtimeClasspath {", "        extendsFrom(custom, configurations.builtIn.get())", "    }", "}");
 	}
 
 	@Test
 	void gradleBuildWithConfigurationCustomizations() throws Exception {
 		GradleBuild build = new GradleBuild();
-		build.customizeConfiguration("runtimeClasspath", (configuration) -> configuration.extendsFrom("custom1"));
-		build.customizeConfiguration("testRuntimeClasspath", (configuration) -> configuration.extendsFrom("custom2"));
+		build.addConfiguration("custom");
+		build.customizeConfiguration("runtimeClasspath", (configuration) -> configuration.extendsFrom("custom"));
+		build.customizeConfiguration("testRuntimeClasspath", (configuration) -> configuration.extendsFrom("builtIn"));
 		List<String> lines = generateBuild(build);
-		assertThat(lines).containsSequence("configurations {", "    runtimeClasspath {", "        extendsFrom(custom1)",
-				"    }", "    testRuntimeClasspath {", "        extendsFrom(custom2)", "    }", "}");
+		assertThat(lines).containsSequence("val custom by configurations.creating", "configurations {",
+				"    runtimeClasspath {", "        extendsFrom(custom)", "    }", "    testRuntimeClasspath {",
+				"        extendsFrom(configurations.builtIn.get())", "    }", "}");
 	}
 
 	@Test