I'm scheduled to get some antibiotic injections into my prostate.

One thing I'm considering doing, is a prostate massage on myself the night before the first injection.

I know how to do it, to the degree that I've done it before and released trapped bacteria. I could feel the difference before and after.

There is reason to believe this would be beneficial in terms of letting the injections kill more bacteria, however could there be any downsides to doing this?

I cannot think of any downside to doing massage prior to prostate injection. However, if the injection is by the transrectal route, after injection you should wait at least a week before resuming massages to allow the injection punctures to completely heal.