COMMENT: Here is the root cause for the problem. I see that the App FEATool which is part of the toolbox behaves differently when compared to other apps. Here is what is going on. 1. Install FEATool from Add-On Explorer. This installs the toolbox with the included App. 2. Check MATLAB path to confirm that only path corresponding to toolbox install folder is added. - /MATLAB Add-Ons/Toolboxes/FEATool Multiphysics Note: Uninstalling the toolbox from Add-On Manager successfully uninstalls both toolbox and app at this point. 3. Now confirm that the App shows up in Apps Gallery. Note: Uninstalling the App from Apps Gallery successfully uninstalls it with no issues at this point. 4.Run the App from Apps Gallery 5. Check MATLAB path and see that the entries on the top include path to FEATool Apps install location /.Add-Ons/Apps/FEAToolMultiphysics /.Add-Ons/Apps/FEAToolMultiphysics/bin /.Add-Ons/Apps/FEAToolMultiphysics/bin/mex /.Add-Ons/Apps/FEAToolMultiphysics/core /.Add-Ons/Apps/FEAToolMultiphysics/ellib /.Add-Ons/Apps/FEAToolMultiphysics/examples /.Add-Ons/Apps/FEAToolMultiphysics/fenics .... Many more 6. close the App 7. Check MATLAB path. MATLAB path entries seen in step 5 still persist even after closing the App! 8. Now try to uninstall the App from Apps Gallery or try to uninstall the toolbox from Add-On Manager. They will fail since the uninstaller fails to uninstall the App because the folders are on MATLAB Path! This behavior can also be seen on Windows with Desktop MATLAB. The expected behavior after closing the App is, the path entries made must be removed. This is the case with most of the other Community Apps. To fix the problem, the App must make sure to clean up MATLAB path on exit. COMMENT: This is caused by the FEATool being a programmatic app. The actual code is P-coded so it is hard for me to have a specific suggestion, but we are unable to hook an oncleanup object to a programmatic app unless the user returns a handle to that app in their startup function. If they return a handle we can attach the oncleanup so that paths are properly managed. There is a tip in the documentation under step 3 on this page that alludes to this behavior: https://www.mathworks.com/help/matlab/creating_guis/app-creation.html COMMENT: As mentioned by Nathan, the app needs to return a handle as part of the startup function to ensure proper cleanup of the App. Including the link to documentation again here (Please refer to step 3) https://www.mathworks.com/help/matlab/creating_guis/app-creation.html I would like to pass on the comments provided by Nathan to the authors of the toolbox. Can you please help me with the same?