Autophagy is a potent cellular degradation pathway, and its activation needs to be tightly controlled. Cargo receptors mediate selectivity during autophagy by bringing cargo to the scaffold protein Atg11 and, in turn, to the autophagic machinery, including the central autophagy kinase Atg1. Here we show how selective autophagy is tightly regulated in space and time to prevent aberrant Atg1 kinase activation and autophagy induction. We established an induced bypass approach (iPass) that combines genetic deletion with chemically induced dimerization to evaluate the roles of Atg13 and cargo receptors in Atg1 kinase activation and selective autophagy progression. We show that Atg1 activation does not require cargo receptors, cargo-bound Atg11, or Atg13 per se. Rather, these proteins function in two independent pathways that converge to activate Atg1 at the vacuole. This pathway architecture underlies the spatiotemporal control of Atg1 kinase activity, thereby preventing inappropriate autophagosome formation. Display omitted •Atg1 activation in selective autophagy is tightly regulated in space and time•Atg1 is activated by the convergence of two independent pathways at the vacuole•Cargo receptors and Atg13 function as tethers for Atg11 and Atg1, respectively•Both cargo receptors and Atg13 can be functionally bypassed in selective autophagy Applying a newly developed synthetic bypass approach (iPass), Torggler et al. show that in selective autophagy, Atg1 kinase is activated at the vacuole by the convergence of two independent pathways. This allows the spatiotemporal control of Atg1 kinase activation.