We investigate QCD amplitudes with massive quarks computed in the four-dimensional helicity scheme (FDH) and dimensional reduction at NNLO and describe how they are related to the corresponding amplitudes computed in conventional dimensional regularization. To this end, the scheme dependence of the heavy quark and the velocity-dependent cusp anomalous dimensions is determined using soft-collinear effective theory. The results are checked against explicit computations of massive form factors in FDH at NNLO. Our results complete the description of the scheme dependence of QCD amplitudes at NNLO