diff --git a/spring-boot-project/spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/ClassPathIndexFile.java b/spring-boot-project/spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/ClassPathIndexFile.java
index b095a85e512..ed11b19f01e 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/ClassPathIndexFile.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/ClassPathIndexFile.java
@@ -72,6 +72,13 @@ final class ClassPathIndexFile {
 		return this.folders.contains(name);
 	}
 
+	boolean containsEntry(String name) {
+		if (name == null || name.isEmpty()) {
+			return false;
+		}
+		return this.lines.contains(name);
+	}
+
 	List<URL> getUrls() {
 		return Collections.unmodifiableList(this.lines.stream().map(this::asUrl).collect(Collectors.toList()));
 	}
diff --git a/spring-boot-project/spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/ExecutableArchiveLauncher.java b/spring-boot-project/spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/ExecutableArchiveLauncher.java
index 514c89b08bd..9ed5fee0aa7 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/ExecutableArchiveLauncher.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/ExecutableArchiveLauncher.java
@@ -101,17 +101,18 @@ public abstract class ExecutableArchiveLauncher extends Launcher {
 
 	@Override
 	protected Iterator<Archive> getClassPathArchivesIterator() throws Exception {
-		Archive.EntryFilter searchFilter = (entry) -> isSearchCandidate(entry) && !isFolderIndexed(entry);
-		Iterator<Archive> archives = this.archive.getNestedArchives(searchFilter, this::isNestedArchive);
+		Archive.EntryFilter searchFilter = this::isSearchCandidate;
+		Iterator<Archive> archives = this.archive.getNestedArchives(searchFilter,
+				(entry) -> isNestedArchive(entry) && !isEntryIndexed(entry));
 		if (isPostProcessingClassPathArchives()) {
 			archives = applyClassPathArchivePostProcessing(archives);
 		}
 		return archives;
 	}
 
-	private boolean isFolderIndexed(Archive.Entry entry) {
+	private boolean isEntryIndexed(Archive.Entry entry) {
 		if (this.classPathIndex != null) {
-			return this.classPathIndex.containsFolder(entry.getName());
+			return this.classPathIndex.containsEntry(entry.getName());
 		}
 		return false;
 	}
diff --git a/spring-boot-project/spring-boot-tools/spring-boot-loader/src/test/java/org/springframework/boot/loader/AbstractExecutableArchiveLauncherTests.java b/spring-boot-project/spring-boot-tools/spring-boot-loader/src/test/java/org/springframework/boot/loader/AbstractExecutableArchiveLauncherTests.java
index 13f0bdea98e..20069b8f912 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-loader/src/test/java/org/springframework/boot/loader/AbstractExecutableArchiveLauncherTests.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-loader/src/test/java/org/springframework/boot/loader/AbstractExecutableArchiveLauncherTests.java
@@ -25,6 +25,7 @@ import java.io.Writer;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.nio.charset.StandardCharsets;
+import java.util.Collections;
 import java.util.Enumeration;
 import java.util.LinkedHashSet;
 import java.util.List;
@@ -52,11 +53,12 @@ public abstract class AbstractExecutableArchiveLauncherTests {
 	File tempDir;
 
 	protected File createJarArchive(String name, String entryPrefix) throws IOException {
-		return createJarArchive(name, entryPrefix, false);
+		return createJarArchive(name, entryPrefix, false, Collections.emptyList());
 	}
 
 	@SuppressWarnings("resource")
-	protected File createJarArchive(String name, String entryPrefix, boolean indexed) throws IOException {
+	protected File createJarArchive(String name, String entryPrefix, boolean indexed, List<String> extraLibs)
+			throws IOException {
 		File archive = new File(this.tempDir, name);
 		JarOutputStream jarOutputStream = new JarOutputStream(new FileOutputStream(archive));
 		jarOutputStream.putNextEntry(new JarEntry(entryPrefix + "/"));
@@ -74,6 +76,9 @@ public abstract class AbstractExecutableArchiveLauncherTests {
 		addNestedJars(entryPrefix, "/lib/foo.jar", jarOutputStream);
 		addNestedJars(entryPrefix, "/lib/bar.jar", jarOutputStream);
 		addNestedJars(entryPrefix, "/lib/baz.jar", jarOutputStream);
+		for (String lib : extraLibs) {
+			addNestedJars(entryPrefix, "/lib/" + lib, jarOutputStream);
+		}
 		jarOutputStream.close();
 		return archive;
 	}
diff --git a/spring-boot-project/spring-boot-tools/spring-boot-loader/src/test/java/org/springframework/boot/loader/JarLauncherTests.java b/spring-boot-project/spring-boot-tools/spring-boot-loader/src/test/java/org/springframework/boot/loader/JarLauncherTests.java
index c894a3480b2..0b265f3a3ef 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-loader/src/test/java/org/springframework/boot/loader/JarLauncherTests.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-loader/src/test/java/org/springframework/boot/loader/JarLauncherTests.java
@@ -20,6 +20,8 @@ import java.io.File;
 import java.net.URL;
 import java.net.URLClassLoader;
 import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
 import java.util.Iterator;
 import java.util.List;
 
@@ -72,7 +74,7 @@ class JarLauncherTests extends AbstractExecutableArchiveLauncherTests {
 
 	@Test
 	void explodedJarShouldPreserveClasspathOrderWhenIndexPresent() throws Exception {
-		File explodedRoot = explode(createJarArchive("archive.jar", "BOOT-INF", true));
+		File explodedRoot = explode(createJarArchive("archive.jar", "BOOT-INF", true, Collections.emptyList()));
 		JarLauncher launcher = new JarLauncher(new ExplodedArchive(explodedRoot, true));
 		Iterator<Archive> archives = launcher.getClassPathArchivesIterator();
 		URLClassLoader classLoader = (URLClassLoader) launcher.createClassLoader(archives);
@@ -80,6 +82,19 @@ class JarLauncherTests extends AbstractExecutableArchiveLauncherTests {
 		assertThat(urls).containsExactly(getExpectedFileUrls(explodedRoot));
 	}
 
+	@Test
+	void jarFilesPresentInBootInfLibsAndNotInClasspathIndexShouldBeAddedAfterBootInfClasses() throws Exception {
+		ArrayList<String> extraLibs = new ArrayList<>(Arrays.asList("extra-1.jar", "extra-2.jar"));
+		File explodedRoot = explode(createJarArchive("archive.jar", "BOOT-INF", true, extraLibs));
+		JarLauncher launcher = new JarLauncher(new ExplodedArchive(explodedRoot, true));
+		Iterator<Archive> archives = launcher.getClassPathArchivesIterator();
+		URLClassLoader classLoader = (URLClassLoader) launcher.createClassLoader(archives);
+		URL[] urls = classLoader.getURLs();
+		List<File> expectedFiles = getExpectedFilesWithExtraLibs(explodedRoot);
+		URL[] expectedFileUrls = expectedFiles.stream().map(this::toUrl).toArray(URL[]::new);
+		assertThat(urls).containsExactly(expectedFileUrls);
+	}
+
 	protected final URL[] getExpectedFileUrls(File explodedRoot) {
 		return getExpectedFiles(explodedRoot).stream().map(this::toUrl).toArray(URL[]::new);
 	}
@@ -93,4 +108,15 @@ class JarLauncherTests extends AbstractExecutableArchiveLauncherTests {
 		return expected;
 	}
 
+	protected final List<File> getExpectedFilesWithExtraLibs(File parent) {
+		List<File> expected = new ArrayList<>();
+		expected.add(new File(parent, "BOOT-INF/classes"));
+		expected.add(new File(parent, "BOOT-INF/lib/extra-1.jar"));
+		expected.add(new File(parent, "BOOT-INF/lib/extra-2.jar"));
+		expected.add(new File(parent, "BOOT-INF/lib/foo.jar"));
+		expected.add(new File(parent, "BOOT-INF/lib/bar.jar"));
+		expected.add(new File(parent, "BOOT-INF/lib/baz.jar"));
+		return expected;
+	}
+
 }