Hybrid systems consisting of different types of qubits are promising for building quantum computers if they combine useful properties of their constituent qubits. However, they also pose additional challenges if one type of qubits is more susceptible to environmental noise than the others. Dynamical decoupling can help to protect such systems by reducing the decoherence due to the environmental noise, but the protection must be designed such that it does not interfere with the control fields driving the logical operations. Here, we test such a protection scheme on a quantum register consisting of the electronic and nuclear spins of a nitrogen-vacancy center in diamond. The results show that processing is compatible with protection: The dephasing time was extended almost to the limit given by the longitudinal relaxation time of the electron spin.