In the adult intestine, intestinal stem cells (ISCs) continually proliferate and differentiate to replenish cells and maintain tissue homeostasis. In this study, Zhouhua Li and colleagues perform an RNAi screen to identify endogenous factors that regulate ISC proliferation in the Drosophila intestine, which is important for understanding tissue homeostasis in health and disease. Here, they identify several subunits of the endoplasmic reticulum (ER) membrane protein complex (EMC), which mediates protein folding and membrane insertion during synthesis in the ER. Indeed, inhibiting EMC function in ISCs leads to excessive proliferation and disruption of intestinal homeostasis. The authors perform co-immunoprecipitation and mass spectrometry experiments to identify candidate interactors of the EMC. Interestingly, they identify Hippo (Hpo), a key component of the Hpo signalling pathway, which has previously been linked to intestinal homeostasis and tumorigenesis. The authors show that the EMC physically interacts with and stabilises Hpo protein, and that Hpo signalling is attenuated in EMC-depleted ISCs. Further, levels of EMC components and Hpo significantly decrease in ISCs of animals treated with tunicamycin (TM), an ER inhibitor that causes accumulation of misfolded proteins. This TM-induced reduction in Hpo levels enhances activation of the downstream component Yorki (Yki), resulting in increased ISC proliferation. Overall, this study reveals an EMC–Hpo–Yki axis that regulates ISC proliferation, and thus intestinal tissue homeostasis, and can explain the increased proliferation observed in TM-treated animals.