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NRT1.1, a nitrate transceptor, plays an important role in nitrate binding, sensing, and nitrate-dependent lateral root (LR) morphology. However, little is known about NRT1.1-mediated nitrate signaling transduction through plasma membrane (PM)-localized proteins. Through in-depth phosphoproteome profiling using membranes of Arabidopsis roots, we identified receptor kinase QSK1 and plasma membrane H+-ATPase AHA2 as potential downstream components of NRT1.1 signaling in a mild low-nitrate (LN)-dependent manner. QSK1, as a functional kinase and molecular link, physically interacts with NRT1.1 and AHA2 at LN and specifically phosphorylates AHA2 at S899. Importantly, we found that LN, not high nitrate (HN), induces formation of the NRT1.1-QSK1-AHA2 complex in order to repress the proton efflux into the apoplast by increased phosphorylation of AHA2 at S899. Loss of either NRT1.1 or QSK1 thus results in a higher T947/S899 phosphorylation ratio on AHA2, leading to enhanced pump activity and longer LRs under LN. Our results uncover a regulatory mechanism in which NRT1.1, under LN conditions, promotes coreceptor QSK1 phosphorylation and enhances the NRT1.1-QSK1 complex formation to transduce LN sensing to the PM H+-ATPase AHA2, controlling the phosphorylation ratio of activating and inhibitory phosphorylation sites on AHA2. This then results in altered proton pump activity, apoplast acidification, and regulation of NRT1.1-mediated LR growth. • Transceptor NRT1.1 is critical for plasma membrane ATPase AHA2 activity under LN • Upon nitrate binding, NRT1.1 promotes coreceptor QSK1 phosphorylation • QSK1 physically links NRT1.1 and AHA2, specifically phosphorylating AHA2 on S899 • NRT1.1-QSK1 transduces LN sensing to AHA2, repressing proton efflux and LR growth Zhu and Krall et al. uncover a mechanism in which NRT1.1, in LN, increases the phosphorylation of QSK1. This forms a complex to transduce LN sensing to the PM H+-ATPase AHA2, regulating the phosphorylation ratio of AHA2 activation and inhibitory phosphorylation sites, resulting in altered apoplast acidification and regulation of LR growth. [ABSTRACT FROM AUTHOR]