For connecting flights, go directly to the gate or check in first?

If you have a transit stopover with a three-hour layover and then a connecting flight, can you go directly to the gate or do you have to go to a check-in counter to confirm that you are on the flight?

Specifically, it is a flight from Frankfurt to Hong Kong and then a connecting flight from Hong Kong to Tokyo.

My last transit stop like this was 29 years ago. I have no idea exactly how it worked back then…