diff --git a/spring-boot-project/spring-boot-docs/src/docs/asciidoc/spring-boot-features.adoc b/spring-boot-project/spring-boot-docs/src/docs/asciidoc/spring-boot-features.adoc
index 222a10612f..2838516a5d 100644
--- a/spring-boot-project/spring-boot-docs/src/docs/asciidoc/spring-boot-features.adoc
+++ b/spring-boot-project/spring-boot-docs/src/docs/asciidoc/spring-boot-features.adoc
@@ -8235,6 +8235,10 @@ For Gradle, refer to the {spring-boot-gradle-plugin-docs}#packaging-layered-jars
 ==== Writing the Dockerfile
 When you create a jar containing the layers index file, the `spring-boot-jarmode-layertools` jar will be added as a dependency to your jar.
 With this jar on the classpath, you can launch your application in a special mode which allows the bootstrap code to run something entirely different from your application, for example, something that extracts the layers.
+
+CAUTION: The `layertools` mode can not be used with a <<deployment.adoc#deployment-install, fully executable Spring Boot archive>> that includes a launch script.
+Disable launch script configuration when building a jar file that is intended to be used with `layertools`.
+
 Here’s how you can launch your jar with a `layertools` jar mode:
 
 [source]
diff --git a/spring-boot-project/spring-boot-tools/spring-boot-jarmode-layertools/src/main/java/org/springframework/boot/jarmode/layertools/ExtractCommand.java b/spring-boot-project/spring-boot-tools/spring-boot-jarmode-layertools/src/main/java/org/springframework/boot/jarmode/layertools/ExtractCommand.java
index 9a3e8b016e..cf159cc29e 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-jarmode-layertools/src/main/java/org/springframework/boot/jarmode/layertools/ExtractCommand.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-jarmode-layertools/src/main/java/org/springframework/boot/jarmode/layertools/ExtractCommand.java
@@ -27,6 +27,7 @@ import java.util.Map;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipInputStream;
 
+import org.springframework.util.Assert;
 import org.springframework.util.StreamUtils;
 import org.springframework.util.StringUtils;
 
@@ -66,6 +67,8 @@ class ExtractCommand extends Command {
 			}
 			try (ZipInputStream zip = new ZipInputStream(new FileInputStream(this.context.getJarFile()))) {
 				ZipEntry entry = zip.getNextEntry();
+				Assert.state(entry != null, "File '" + this.context.getJarFile().toString()
+						+ "' is not compatible with layertools; ensure jar file is valid and launch script is not enabled");
 				while (entry != null) {
 					if (!entry.isDirectory()) {
 						String layer = this.layers.getLayer(entry);
diff --git a/spring-boot-project/spring-boot-tools/spring-boot-jarmode-layertools/src/test/java/org/springframework/boot/jarmode/layertools/ExtractCommandTests.java b/spring-boot-project/spring-boot-tools/spring-boot-jarmode-layertools/src/test/java/org/springframework/boot/jarmode/layertools/ExtractCommandTests.java
index 13646be6be..898a668481 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-jarmode-layertools/src/test/java/org/springframework/boot/jarmode/layertools/ExtractCommandTests.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-jarmode-layertools/src/test/java/org/springframework/boot/jarmode/layertools/ExtractCommandTests.java
@@ -18,6 +18,7 @@ package org.springframework.boot.jarmode.layertools;
 
 import java.io.File;
 import java.io.FileOutputStream;
+import java.io.FileWriter;
 import java.io.IOException;
 import java.util.Arrays;
 import java.util.Collections;
@@ -32,6 +33,7 @@ import org.mockito.Mock;
 import org.mockito.MockitoAnnotations;
 
 import static org.assertj.core.api.Assertions.assertThat;
+import static org.assertj.core.api.Assertions.assertThatIllegalStateException;
 import static org.mockito.BDDMockito.given;
 
 /**
@@ -95,6 +97,19 @@ class ExtractCommandTests {
 		assertThat(new File(this.extract, "c/c/c.jar")).exists();
 	}
 
+	@Test
+	void runWithJarFileContainingNoEntriesFails() throws IOException {
+		File file = new File(this.temp, "empty.jar");
+		FileWriter writer = new FileWriter(file);
+		writer.write("text");
+		writer.flush();
+		given(this.context.getJarFile()).willReturn(file);
+		given(this.context.getWorkingDir()).willReturn(this.extract);
+		assertThatIllegalStateException()
+				.isThrownBy(() -> this.command.run(Collections.emptyMap(), Collections.emptyList()))
+				.withMessageContaining("not compatible with layertools");
+	}
+
 	private File createJarFile(String name) throws IOException {
 		File file = new File(this.temp, name);
 		try (ZipOutputStream out = new ZipOutputStream(new FileOutputStream(file))) {