During mating, males provide females with seminal fluids that include proteins affecting female physiology and, in some cases, reproductive behavior. In several species these male-derived modulators of reproduction are processed upon transfer to the female, suggesting molecular interaction between the sexes. Males could increase their reproductive success by contributing to regulation of this processing; consistent with this hypothesis, seminal fluids are rich in proteolysis regulators. However, whether these molecules carry out processing of male-derived reproductive modulators is unknown. We tested for this role using RNAi to knock down individually 11 Drosophila seminal fluid proteases and protease inhibitors. We found that CG11864, a predicted astacin-type metalloprotease in seminal fluid, is necessary to process two other seminal proteins: the ovulation hormone ovulin (Acp26Aa) and the sperm storage protein Acp36DE. This processing occurs only after all three proteins have entered the female. Moreover, CG11864 itself is processed inside males while en route to the female and before its action in processing ovulin and Acp36DE. Thus, processing of seminal proteins is stepwise in Drosophila , beginning in the male after the proteins leave their site of synthesis and continuing within another organism, the mated female, and the male-donated protease CG11864 is an agent of this latter processing.