This chapter highlights the critical role of the silkworm (Bombyx mori) expression system in producing complex eukaryotic proteins with proper post-translational modifications, a major advantage over prokaryotic hosts. The system’s capacity for accurate disulfide bond formation was demonstrated using porcine insulin-like peptide 3 (pINSL3), which correctly folded and exhibited full biological activity. Furthermore, the system supports complex regulatory modifications, evidenced by the successful expression of human acetyl-CoA carboxylase 2 (hACC2) and malonyl-CoA decarboxylase (hMCD). These lipid metabolism enzymes underwent appropriate biotinylation and phosphorylation, ensuring the functional integrity and precise allosteric regulation of their catalytic activities. Finally, the chapter addresses the inherent limitations of insect N-glycosylation pathways, which typically yield paucimannosidic structures. By coexpressing human immunoglobulin G (hIgG) with human glycosyltransferases (hGnT II and hGalT I) under the polh promoter, the silkworm system was successfully engineered to produce biantennary, terminally galactosylated complex N-glycans. Collectively, these findings validate the silkworm as a highly effective, scalable biofactory capable of executing advanced post-translational modifications—including disulfide bridge formation, phosphorylation, and mammalian-like glycosylation—essential for the structural and functional viability of biopharmaceuticals.