We present a method to quantify quantum correlations in arbitrary systems of indistinguishable fermions using witness operators. The method associates the problem of finding the optimal entanglement witness of a state with a class of problems known as semidefinite programs (SDPs), which can be solved efficiently with arbitrary accuracy. Based on these optimal witnesses, we introduce a measure of quantum correlations which has an interpretation analogous to the Generalized Robustness of entanglement. We also extend the notion of quantum discord to the case of indistinguishable fermions, and propose a geometric quantifier, which is compared to our entanglement measure. Our numerical results show a remarkable equivalence between the proposed Generalized Robustness and the Schliemann concurrence, which are equal for pure states. For mixed states, the Schliemann concurrence presents itself as an upper bound for the Generalized Robustness. The quantum discord is also found to be an upper bound for the entanglement.