Since the Caech Republic is in Schengen, if you are arriving in Frankfurt from outside the Schengen area, you will at least have to go through immigration.

Dunno about customs.

You will also go through what is possibly the most humiliating security check in the developed world, regardless of whether you go through immigration or not. If you take a vitamin pill which contains iron, that's enough to set off the magnetometer. In addition to all the usual stuff, they will then take away your wallet, passport, boarding pass, and everything else they can. It will all accumulate at the end of the belt, where lots of other passengers and employees have access, while they are wanding you in a thorough and leisurely manner.