Yes, you do that in the permission schemes and roles for the projects.
You've probably got a line in there that says "browse project = role users" and then in the roles, the projects have "JIRA software users". That grants access to everyone who can log in.
The best option is probably to remove the group "JIRA Software users" from the role of users, and then, for each project add back each of the groups that need access to the project. Leaving the others out means they won't get the browse access which means they won't see the project.
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