Difficult to run multi company with access rights?

I have been trying to setup multi company with User A ---->Company A & User B —> Company B access for all data including customers,items,invoices and reports

It has grown to be very complicated with a growing list of User Permissions to be set.

How others are handling such very obvious things .Can any one enlighten me ?

If both the companies are absolutely separate, with different user-base, you should create a separate ERPNext instance for them.

In the user Permission, if you check “Restrict for all roles of this user”, then “Apply User Permission” will be enabled for all the roles of that User. Perhaps you will have to untick it for the doctypes (like Items, Customer, Supplier etc.) on which you don’t want to apply permissions.