The precise and automated calibration of quantum gates is a key requirement for building a reliable quantum computer. Unlike errors from decoherence, systematic errors can in principle be completely removed by tuning experimental parameters. Here, we present an iterative calibration routine which can remove systematic gate errors on several qubits. A central ingredient is the construction of pulse sequences that extract independent indicators for every linearly independent error generator. We show that decoherence errors only moderately degrade the achievable infidelity due to systematic errors. Furthermore, we investigate the convergence properties of our approach by performing simulations for a specific qubit encoded in a pair of spins. Our results indicate that a gate set with 230 gate parameters can be calibrated in about ten iterations, after which incoherent errors limit the gate fidelity.