We study in detail the impact of the current uncertainty in nucleon matrix elements on the sensitivity of direct and indirect experimental techniques for dark matter detection. We perform two scans in the framework of the cMSSM: one using recent values of the pion-sigma term obtained from Lattice QCD, and the other using values derived from experimental measurements. The two choices correspond to extreme values quoted in the literature and reflect the current tension between different ways of obtaining information about the structure of the nucleon. All other inputs in the scans, astrophysical and from particle physics, are kept unchanged. We use two experiments, XENON100 and IceCube, as benchmark cases to illustrate our case. We find that the interpretation of dark matter search results from direct detection experiments is more sensitive to the choice of the central values of the hadronic inputs than the results of indirect search experiments. The allowed regions of cMSSM parameter space after including XENON100 constrains strongly differ depending on the assumptions on the hadronic matrix elements used. On the other hand, the constraining potential of IceCube is almost independent of the choice of these values.