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Hi RobConn, there is no function built into the managed version of the program to delete the quarantine. We actually do not recommend that you delete your quarantine items in case of needing to restore something if there is a false positive. The infections that are placed in quarantine are stripped and encrypted, leaving them no chance to run. They are safe there and do not take much space at all. If you do wish to delete the quarantine, you will need to create a script to delete the contents of C:\ProgramData\Malwarebytes\Malwarebytes' Anti-Malware\Quarantine on your endpoints.

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