The Nitrogen Vacancy Center in diamond coupled to addressable surrounding nuclear spins forms a versatile building block for future quantum technologies. While previous activities focused on sensing with only a single or very few spins in operation, recently multi-qubit registers have been successfully implemented for quantum information processing. Further progress requires a detailed understanding of the performance of quantum protocols for consecutive gate operations and thus, beyond established treatments for relaxation and dephasing. Here, we provide such a theoretical analysis for a small spin registers with up to four spins built out of NV and environmental constituents in presence of ensembles of interacting impurity spins. Adapting a cluster correlation expansion, we predict coherence properties as well as fidelities for GHZ- and Bell-gate operations also in presence of decoupling pulses. The influence of the volume density and the geometry of the spin-bath consisting of substitutional nitrogen atoms are also taken into account.