Mitofusin-1 (MFN1) and Mitofusin-2 (MFN2) are key players in mitochondrial fusion, endoplasmic reticulum (ER)-mitochondria yuxtaposition, and autophagy. However, the mechanisms by which these proteins participate in these processes remain poorly understood. To better understand their functions, we studied the interactomes of these two proteins. To this end, we used CRISPR/Cas9 technology to insert an HA-tag in the C-terminal domain of MFN1 and MFN2 and generated HeLa cell lines that endogenously expressed MFN1-HA or MFN2-HA, respectively. HA-pulldown followed by mass spectrometry identified potential interactors of MFN1 and MFN2. A substantial proportion of interactors were common for MFN1 and MFN2 and were regulated by nutrient deprivation. We validated novel ER and endosomal partners of MFN1 and/or MFN2 with a potential role in interorganelle communication. We characterized RAB5C as an endosomal modulator of mitochondrial dynamics through its interaction with MFN1 and SLC27A2 as a novel partner of MFN2 relevant in autophagy. Our findings reveal that MFN proteins participate in nutrient-modulated pathways involved in organelle communication.