Assuming you're talking about using Malwarebytes on Windows, Malwarebytes is a great on-demand scanner, but you should disable its real-time protection. If real-time protection was turned on automatically because it gave you a premium trial, you can disable it in the settings. If I were you, I would disable the whole premium trial.
When running an on-demand scan, however, you can expect some slowdowns while it's completing its scan.
For real-time protection, I recommend just using Windows Defender. It's efficient, out of the way, and has consistently been blocking 100% of real-world threats in the latest tests.