I'm trying to get an app notarized, which fails with this error: The signature of the binary is invalid. However, locally checking the signature does succeed: $ codesign -vvv --deep --strict TheApp.app […] TheApp.app: valid on disk TheApp.app: satisfies its Designated Requirement Performing this check on every single item in the app's MacOS folder also succeeds. Context: embedded prebuilt binaries Now, the app has something unusual about it: it embeds prebuilt binaries, arranged in various nested folders. So, the app bundle's MacOS folder actually contains another folder with a whole tree of executables and libraries: Removing these (before building) does fix the notarization issue, but obviously I'd like to keep them in. I did my best to properly sign these items: At build time, they're copied into the product by a Copy Files phase (but not signed), then signed by a script phase That signing uses the same signing identity as the running Xcode build, and enables the hardened runtime The app builds an