Autophagy is a mechanism by which intracellular cargo are catabolised in the lysosome. It involves the formation of double membraned organelles termed autophagosomes, a complex process orchestrated by the serine/threonine kinase ULK complex and class III PI3 kinase VPS34. Unbiased screens for ULK substrates revealed that the phosphoproteome is significantly altered upon loss of Ulk1/2 and yielded a high confidence list of substrates, including VPS34 complex member VPS15 and AMPK complex member PRKAG2. We identified 6 new ULK substrate residues in the VPS15. Mutation of these VPS15 phosphoacceptors reduces autophagosome formation and autophagic flux in cells, and VPS34 activity in vitro. ULK phosphorylation of the major phosphosite in VPS15, serine 861, decreases both autophagy initiation and autophagic flux. Analysis of VPS15 knockout cells and the ULK substrate VPS34 serine 249 revealed two novel ULK-dependent phenotypes downstream of VPS15 removal: starvation-independent accumulation of ULK substrates and kinase activity-regulated recruitment of autophagy proteins to ubiquitin-positive structures, both of which occur upon VPS15 ablation and can be partially recapitulated by chronic VPS34 inhibition.