diff --git a/Ghidra/Framework/Utility/src/main/java/ghidra/GhidraApplicationLayout.java b/Ghidra/Framework/Utility/src/main/java/ghidra/GhidraApplicationLayout.java
index 6a025ca072..31423b8833 100644
--- a/Ghidra/Framework/Utility/src/main/java/ghidra/GhidraApplicationLayout.java
+++ b/Ghidra/Framework/Utility/src/main/java/ghidra/GhidraApplicationLayout.java
@@ -168,6 +168,11 @@ public class GhidraApplicationLayout extends ApplicationLayout {
 								extensionModuleDir))) {
 						continue;
 					}
+					// Skip extensions slated for cleanup
+					if (new File(extensionModuleDir, ModuleUtilities.MANIFEST_FILE_NAME_UNINSTALLED)
+							.exists()) {
+						continue;
+					}
 
 					moduleRootDirectories.add(new ResourceFile(extensionModuleDir));
 				}