Interacts with BCL2 and BCL2L1 (By similarity). Interacts with GOPC and GRID2. Interacts with AMBRA1. Forms a complex with PIK3C3 and PIK3R4 and either UVRAG and KIAA0226/Rubicon, or with ATG14. UVRAG and ATG14 form mutually exclusive complexes through direct competition for BECN1-binding. The complex containing ATG14 upregulates autophagy, while the one containing Rubicon downregulates autophagy (By similarity). Interacts with VMP1 (By similarity). Interacts with PIK3CB.