Significance Seminal fluid plays a critical role in reprogramming female physiology and behavior to promote male reproductive success. We show, in the fruit fly, that specific seminal proteins, including the archetypal “female-reprogramming” molecule Sex Peptide, are stored in male seminal secretions in association with large neutral lipid-containing microcarriers, which rapidly disperse in females. Related structures are also observed in other Sex Peptide-expressing Drosophila species. Males lacking Sex Peptide have structurally defective microcarriers and exhibit abnormal transfer of many seminal proteins to females. Our data reveal that this key signaling molecule in Drosophila seminal fluid is also a microcarrier assembly factor that modulates transfer of other seminal factors and that this may be a more evolutionarily ancient role of this protein.