ABA signaling and transport play important roles in plant systematic responses to environmental factors. Previously, we reported that C-terminally encoded peptide receptor 2 (CEPR2) balances plant growth and ABA responses by phosphorylating abscisic acid (ABA) receptors. Here, we showed that CEPR2 also directly phosphorylated the ABA transporter NRT1.2 by phosphaproteomics analysis using CEPR2 overexpression line and by physiological and biochemical experiments. Using transgenic seedlings, we demonstrated that NRT1.2 positively regulated the ABA response, and that CEPR2 acted on NRT1.2 epistatically. Specifically, CEPR2 phosphorylated NRT1.2 at serine 292 (Ser292) to promote the degradation of NRT1.2 via the 26S proteasome and vacuolar degradation pathways. However, ABA strongly inhibited the phosphorylation of NRT1.2 at Ser292, stabilizing NRT1.2. Transportation assays in yeast and Xenopus oocytes showed that the nonphosphorylation of NRT1.2 showed high ABA but very low nitrate import activity, while the phosphorylation of NRT1.2 by CEPR2 eliminated NRT1.2-mediated ABA import but slightly increased nitrate transport. These findings were consistent with our analyses of complement mutants in planta. Thus, our results provide detailed mechanisms of NRT1.2 in transporting ABA and nitrate in response to environmental conditions in plants. Besides, it is a better way for plants to overexpress the unphosphorylated NRT1.2 at Ser292 both under high and low nitrate conditions.