We calculate the high and low scale threshold corrections to the D=6 proton decay mode in supersymmetric SU(5) grand unified theories with higher-dimensional representation Higgs multiplets. In particular, we focus on a missing-partner model in which the grand unified group is spontaneously broken by the 75-dimensional Higgs multiplet and the doublet–triplet splitting problem is solved. We find that in the missing-partner model the D=6 proton decay rate gets suppressed by about 60%, mainly due to the threshold effect at the GUT scale, while the SUSY-scale threshold corrections are found to be less prominent when sfermions are heavy.