The speculation from @eskimo was very insightful, after installing several plugins code sign does indeed show many modified files (and the application refuses to start). In my case this was due to installing plugins from the eclipse marketplace. This does point the way towards an easier workaround: Verify seal is broken: codesign -v -vvv --deep /Applications/Eclipse.app /Applications/Eclipse.app: invalid Info.plist (plist or signature have been modified) In architecture: x86_64 Sign the modified Eclipse.app % sudo codesign --force --sign -  /Applications/Eclipse.app /Applications/Eclipse.app: replacing existing signature Verify seal is restored: % codesign -v -vvv --deep /Applications/Eclipse.app/Eclipse.app /Applications/Eclipse.app/Eclipse.app: valid on disk /Applications/Eclipse.app/Eclipse.app: satisfies its Designated Requirement This is still a workaround, but beats reinstalling from scratch (and reinstalling eclipse plugins).