Among certification techniques, those based on the violation of Bell inequalities are appealing because they do not require assumptions on the underlying Hilbert space dimension and on the accuracy of calibration methods. Such device-independent techniques have been proposed to certify the quality of entangled states, unitary operations, projective measurements following von Neumanns model and rank-one positive-operator-valued measures (POVM). Here, we show that they can be extended to the characterization of quantum instruments with post-measurement states that are not fully determined by the Kraus operators but also depend on input states. We provide concrete certification recipes that are robust to noise.