Can you have multi-site WP and keep users separate?

No, in a multisite, all sites have the same users table and user meta.

Keep in mind if you did manage this though, it would be trivial for them to find out it was a multisite based on code, and they could very easily break out of their site.

As an aside, you could run filters to strip out everything that makes multisite multisite, and make the user tables separate, but:

  • now the only benefit is that creating sites is easier
  • Network admin roles and capabilities will be broken
  • Any plugins or themes that do anything remotely related to multisite will reveal the truth, unavoidably
  • The entire setup would require ongoing updates and maintenance to fix issues
  • Plugin compatibility problems and bugs
  • Issue with cookies and domains
  • The Network admin user panel would be useless if not broken
  • Any plugin that uses switch_to_blog could cause data corruption, including navigation in the network admin
  • A lot of additional code would need writing to setup new users etc, and create the existing tables with the new prefixes
  • Every user related API would need modifying

I estimate at least a months worth of work from an experienced developer, with an extended maintenance contract. Longer for the average developer, with no guarantee it will work well.

Or you could write a script that lists WP instances and lets you download and install new ones. Better yet, use WP docker images and provision them automatically.

This is a classic XY problem. You have a problem “How do I spin up WP installs quickly so I can resell them”, but rather than ask that question, you devised a solution and asked how to implement the solution instead

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