Membrane trafficking, organelle biogenesis and function play important roles in regulating protein homeostasis in the cells that are essential for plant growth and development, as well as responses to external signals. The plant endomembrane system contains several functionally distinct membrane-enclosed organelles, including the endoplasmic reticulum (ER), Golgi apparatus, trans-Golgi network (TGN) or early endosomes (EE), prevacuolar compartment (PVC) or multivesicular body (MVB) and vacuole. The plant endomembrane system also crosstalk with the autophagic pathway involving in the formation of autophagosome and engulfment of cytosolic contents for subsequent degradation upon autophagosome-vacuole fusion in plants. The endosomal sorting complex required for transport (ESCRT) machinery mediates the formation of intraluminal vesicles (ILVs) in MVBs as well as the sorting of the ubiquitinated cargoes into the ILVs of MVBs for vacuolar degradation. we have characterized a plant unique ESCRT component termed FYVE domain protein required for endosomal sorting 1 (FREE1) and demonstrated that FRFF1 plays multiple functions with distinct underlying mechanisms in plants, including regulation of MVB/vacuole biogenesis, crosstalk of the endomembrane system with the autophagic pathway, peroxisome-mediated degradation of lipid droplets (LDs) in germinating seedlings, and autophagosome closure under stress condition. Here I will summarize our major findings and present an update on the multi-functions of FREE1 in regulating membrane trafficking, protein homeostasis, organelle biogenesis and function in plants. Supported by grants from the Research Grants Council (RGC) of Hong Kong and CUHK.