diff --git a/src/main/java/net/fabricmc/loom/configuration/mods/ModProcessor.java b/src/main/java/net/fabricmc/loom/configuration/mods/ModProcessor.java
index 54402cace..5efb674d1 100644
--- a/src/main/java/net/fabricmc/loom/configuration/mods/ModProcessor.java
+++ b/src/main/java/net/fabricmc/loom/configuration/mods/ModProcessor.java
@@ -121,6 +121,12 @@ private String describeConfiguration(Configuration configuration) {
 	}
 
 	private void stripNestedJars(Path path) {
+		try {
+			ZipUtils.deleteIfExists(path, "META-INF/jarjar/metadata.json");
+		} catch (IOException e) {
+			throw new UncheckedIOException("Failed to strip nested jars from %s".formatted(path), e);
+		}
+
 		if (!ZipUtils.contains(path, "fabric.mod.json")) {
 			if (ZipUtils.contains(path, "quilt.mod.json")) {
 				// Strip out all contained jar info as we dont want loader to try and load the jars contained in dev.
diff --git a/src/main/java/net/fabricmc/loom/util/ZipUtils.java b/src/main/java/net/fabricmc/loom/util/ZipUtils.java
index 2d1be1e68..14c5cce57 100644
--- a/src/main/java/net/fabricmc/loom/util/ZipUtils.java
+++ b/src/main/java/net/fabricmc/loom/util/ZipUtils.java
@@ -184,6 +184,12 @@ public static void replace(Path zip, String path, byte[] bytes) throws IOExcepti
 		}
 	}
 
+	public static void deleteIfExists(Path zip, String path) throws IOException {
+		try (FileSystemUtil.Delegate fs = FileSystemUtil.getJarFileSystem(zip, false)) {
+			Files.deleteIfExists(fs.getPath(path));
+		}
+	}
+
 	public static int transformString(Path zip, Collection<Pair<String, UnsafeUnaryOperator<String>>> transforms) throws IOException {
 		return transformString(zip, transforms.stream());
 	}