diff --git a/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/main/java/org/springframework/boot/loader/tools/AbstractJarWriter.java b/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/main/java/org/springframework/boot/loader/tools/AbstractJarWriter.java
index d5cdcdda26..3cbf908346 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/main/java/org/springframework/boot/loader/tools/AbstractJarWriter.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/main/java/org/springframework/boot/loader/tools/AbstractJarWriter.java
@@ -209,13 +209,21 @@ public abstract class AbstractJarWriter implements LoaderClassesWriter {
 		try (JarInputStream inputStream = new JarInputStream(new BufferedInputStream(loaderJar.openStream()))) {
 			JarEntry entry;
 			while ((entry = inputStream.getNextJarEntry()) != null) {
-				if (entry.getName().endsWith(".class")) {
+				if (isDirectoryEntry(entry) || isClassEntry(entry)) {
 					writeEntry(new JarArchiveEntry(entry), new InputStreamEntryWriter(inputStream));
 				}
 			}
 		}
 	}
 
+	private boolean isDirectoryEntry(JarEntry entry) {
+		return entry.isDirectory() && !entry.getName().equals("META-INF/");
+	}
+
+	private boolean isClassEntry(JarEntry entry) {
+		return entry.getName().endsWith(".class");
+	}
+
 	private void writeEntry(JarArchiveEntry entry, EntryWriter entryWriter) throws IOException {
 		writeEntry(entry, entryWriter, UnpackHandler.NEVER);
 	}
diff --git a/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/test/java/org/springframework/boot/loader/tools/RepackagerTests.java b/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/test/java/org/springframework/boot/loader/tools/RepackagerTests.java
index c92e043148..1e632563c8 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/test/java/org/springframework/boot/loader/tools/RepackagerTests.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/test/java/org/springframework/boot/loader/tools/RepackagerTests.java
@@ -20,7 +20,10 @@ import java.io.File;
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
+import java.nio.file.attribute.FileTime;
 import java.nio.file.attribute.PosixFilePermission;
+import java.time.OffsetDateTime;
+import java.time.ZoneOffset;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Enumeration;
@@ -156,6 +159,36 @@ class RepackagerTests extends AbstractPackagerTests<Repackager> {
 		}
 	}
 
+	@Test
+	void allLoaderDirectoriesAndFilesUseSameTimestamp() throws IOException {
+		this.testJarFile.addClass("A.class", ClassWithMainMethod.class);
+		Repackager repackager = createRepackager(this.testJarFile.getFile(), true);
+		Long timestamp = null;
+		repackager.repackage(this.destination, NO_LIBRARIES);
+		for (ZipArchiveEntry entry : getAllPackagedEntries()) {
+			if (entry.getName().startsWith("org/springframework/boot/loader")) {
+				if (timestamp == null) {
+					timestamp = entry.getTime();
+				}
+				else {
+					assertThat(entry.getTime()).withFailMessage("Expected time %d to be equal to %d for entry %s",
+							entry.getTime(), timestamp, entry.getName()).isEqualTo(timestamp);
+				}
+			}
+		}
+	}
+
+	@Test
+	void allEntriesUseProvidedTimestamp() throws IOException {
+		this.testJarFile.addClass("A.class", ClassWithMainMethod.class);
+		Repackager repackager = createRepackager(this.testJarFile.getFile(), true);
+		long timestamp = OffsetDateTime.of(2000, 1, 1, 0, 0, 0, 0, ZoneOffset.UTC).toInstant().toEpochMilli();
+		repackager.repackage(this.destination, NO_LIBRARIES, null, FileTime.fromMillis(timestamp));
+		for (ZipArchiveEntry entry : getAllPackagedEntries()) {
+			assertThat(entry.getTime()).isEqualTo(timestamp);
+		}
+	}
+
 	private boolean hasLauncherClasses(File file) throws IOException {
 		return hasEntry(file, "org/springframework/boot/")
 				&& hasEntry(file, "org/springframework/boot/loader/JarLauncher.class");