Abstract Secretory cells in glands and the nervous system frequently package and store proteins destined for regulated secretion in dense-core granules (DCGs), which disperse when released from the cell surface. Despite the relevance of this dynamic process to diseases such as diabetes and human neurodegenerative disorders, our mechanistic understanding is relatively limited, because of the lack of good cell models to follow the nanoscale events involved. Here, we employ the prostate-like secondary cells (SCs) of the Drosophila male accessory gland to dissect the cell biology and genetics of DCG biogenesis. These cells contain unusually enlarged DCGs, which are assembled in compartments that also form secreted nanovesicles called exosomes. We demonstrate that known conserved regulators of DCG biogenesis, including the small G-protein Arf1 and the coatomer complex AP-1, play key roles in making SC DCGs. Using real-time imaging, we find that the aggregation events driving DCG biogenesis are accompanied by a change in the membrane associated small Rab GTPases which are major regulators of membrane and protein trafficking in the secretory and endosomal systems. Indeed, a transition from trans -Golgi Rab6 to recycling endosomal protein Rab11, which requires conserved DCG regulators like AP-1, is essential for DCG and exosome biogenesis. Our data allow us to develop a model for DCG biogenesis that brings together several previously disparate observations concerning this process and highlights the importance of communication between the secretory and endosomal systems in controlling regulated secretion. Author summary Cells communicate with each other by releasing signalling molecules that bind receptors on target cells and alter their behaviour. Before their release, these signals are typically stored in condensed structures called dense-core granules (DCGs). DCGs are found in many animal species and their dysregulation is linked to several major human diseases, such as diabetes and neurodegenerative disorders. However, the mechanisms controlling DCG formation and secretion are only partly understood. Here we study this process in fruit flies using a secretory cell, which contains unusually large DCGs. We show that known regulators of DCG formation in mammals also control DCG production in these fly cells and identify new DCG assembly steps by following the process in living cells. Furthermore, we show that the cell’s secretory and recycling endosomal compartments must interact to induce the rapid condensation of proteins into a DCG, and that known regulators of DCG formation are needed for this crucial event to take place. Our work provides a platform from which to work out the molecular mechanisms that enable this critical secretory-endosomal interaction and probe its roles in diseases of secretion.