Managing plugin updates to database with version control

We are starting to implement a version control process for our clients’ WP sites. The plan is to have local environments for the sites and repositories for each site that house the theme files and plugin files only. This is pretty standard process from our understanding. We are not using any sort of version control plugin and the staging and local databases will be completely separate because version controlling a database is very hard to manage correctly.

But a question has come up with when you update a plugin on local, and that plugin makes some modifications to the database. But when we push the changes to the staging server, the old plugin files are simply getting overridden by the push. There is never any update scripts ran like you would if you were to manually update each plugin form the admin panel. So how do you manage a change to the database structure that a plugin makes on update when we’re only pushing files?