We examine the detailed scenario for implementing n control qubit Toffoli gates and select gates on ion trap quantum computers, especially those that shuttle ions into interaction zones. We determine expected performance of these gates with realistic parameters for an ion trap quantum computer and taking into account the time variation of the exchange integrals. This allows us to estimate the errors due to spin–phonon entanglement as well. While there are challenges with implementing these gates, because their performance always has some degree of error, they should be feasible on current hardware, but they may be too slow to be used efficiently in quantum codes on noisy intermediate scale quantum computers. Here, we estimate these gate times for Yb based ion trap quantum computers.