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I know that using GPO one can deploy trusted CA certificates to client computers and then deploy it to "Trusted Publishers" certificate store. I want to know if there is some other way by which i can deploy trusted CA certificates to a different certificate store?? I also wanted to know if i can remove such trusted certificates from clients via GPO?? any help regrading this will be highly appreciated.
In that case, i will like to share that certificates deployed through "Trusted Root Certification Authorities" setting in GPO goes in to the store with exactly the same name on clients. Its the only store that can be chosen, you wont be able to chose any other one. In order to get better idea of "Trusted Root Certification Authorities" and "Trusted Publisher" store just go through the below articles.
Trusted Root Certification Authorities Certificate Store
Trusted Publishers Certificate Store
You wont be able to remove a certificate via GPO but you can use Certificate Manager Tool for that.
Certificate Manager Tool (Certmgr.exe)