NADPH oxidase activator 1 (NOXA1) together with NADPH oxidase organizer 1 (NOXO1) are key regulatory subunits of the NADPH oxidase NOX1. NOX1 is expressed mainly in colon epithelial cells and could be involved in mucosal innate immunity by producing reactive oxygen species (ROS). Contrary to its phagocyte counterpart NOX2, the mechanisms involved in NOX1 activation and regulation remain unclear. Here we report that NOX1 activity is regulated through MAP kinase (MAPK), protein kinase C (PKC), and protein kinase A (PKA)-dependent phosphorylation of NOXA1. We identified Ser-282 as target of MAPK and Ser-172 as target of PKC and PKA in vitro and in a transfected human embryonic kidney 293 (HEK293) cell model using site directed mutagenesis and phosphopeptide mapping analysis. In HEK293 cells, phosphorylation of these sites occurred at a basal level and down-regulated constitutive NOX1 activity. Indeed, S172A and S282A single mutants of NOXA1 significantly up-regulated constitutive NOX1-derived ROS production, and S172A/S282A double mutant further increased it, as compared to wild-type NOXA1. Furthermore, phosphorylation of NOXA1 on Ser-282 and Ser-172 decreased its binding to NOX1 and Rac1. These results demonstrated a critical role of NOXA1 phosphorylation on Ser-282 and Ser-172 in preventing NOX1 hyperactivation through the decrease of NOXA1 interaction to NOX1 and Rac1.