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Abstract We extend the already existing two-loop calculation of the effective bottom-Yukawa coupling in the MSSM. In addition to the resummation of the dominant corrections for large values of tg $$\beta $$ β , we include the subleading terms related to the trilinear Higgs coupling $$A_b$$ A b and contributions induced by the electroweak gauge couplings. This calculation has been extended to the NNLO corrections to the MSSM strange-Yukawa coupling. Our analysis leads to residual theoretical uncertainties of the effective Yukawa couplings at the per-cent level.