We investigate the regularization-scheme dependence of scattering amplitudes in massless QCD and find that the four-dimensional helicity scheme (FDH) and dimensional reduction (DRED) are consistent at least up to NNLO in the perturbative expansion if renormalization is done appropriately. Scheme dependence is shown to be deeply linked to the structure of UV and IR singularities. We use jet and soft functions defined in soft-collinear effective theory (SCET) to efficiently extract the relevant anomalous dimensions in the different schemes. This result allows us to construct transition rules for scattering amplitudes between different schemes (CDR, HV, FDH, DRED) up to NNLO in massless QCD. We also show by explicit calculation that the hard, soft and jet functions in SCET are regularization-scheme independent.