We are flying from Orlando to Amsterdam with a connection in Frankfurt. It is on Lufthansa(1 ticket). If we are not using the 2nd flight, will our bags still go to Amsterdam or is there a way to just check them to Frankfurt? Any advice would be greatly appreciated.

Generally, no, and if this is a round trip/return ticket, note the return portions will be canceled once you've skipped the FRA-AMS flight.

Just to clarify . . . it is a compound question >>will our bags still go to Amsterdam or is there a way to just check them to Frankfurt?<<.

Gardyloo was responding to the sencond part - no you can't get them at Frankfurt.

As he says it is a BIG problem/mistake if this is a R-T booking. Not only will your bags be in Amsterdam while you are in Frankfurt . . . you will not have a flight home. Did you do this to save $$ or did your plans change after booking? Paying the change fees and higher fare might be worthwhile if Frankfurt is your actual destination.

And . . . If this is not a R-T booking and there is no flight home to lose -- then you will have to travel carry-on only.

Thank you both for pointing out the issue with the return ticket. I will amend the flight to make sure we don't end up stranded!