This is similar to the question at Deploying QGIS settings in an enterprise environment – We are looking to copy the QGIS settings from a preconfigured user to new users on a Citrix server.
The answer there suggests copying and pasting the .qgis2 folder and exporting and importing the relevant registry settings.
On the Citrix server registry, while the QGIS application is open for a specific user, we have registry folders for that user, including the path as follows: 'session/user ID'\Software\QGIS\QGIS2\Qgis
The Qgis folder has the settings that you would find in the QGIS menu bar under Settings > Options
However, when the application is closed, the whole session disappears from the registry. The option of importing the registry folders for a user may be unfeasible, because the session/user ID folders exist only when the user has the application open.
If we re-open the application for this user, the settings are retained, so they must be stored somewhere, but these settings are not stored in the .qgis2 folder.
We have considered the possibility of importing the folders for a user while their session is open, but the user/session ID is just a long string of letters, numbers, and hyphens, and it is difficult to identify the correct session even when there are only a couple of them open in testing, so it might be quite unfeasible when there are more open after deployment to more users.
The answer at QGIS keeping settings in sync? suggests that the settings are stored in a file called QGIS2.ini - but we cannot find any file of that name either.