Atrial natriuretic peptide (ANP), via its guanylyl cyclase A (GC‐A) receptor and intracellular guanosine 3′,5′‐cyclic monophosphate production, is critically involved in the regulation of blood pressure. In patients with chronic heart failure, the plasma levels of ANP are increased, but the cardiovascular actions are severely blunted, indicating a receptor or postreceptor defect. Studies on metabolically labelled GC‐A‐overexpressing cells have indicated that GC‐A is extensively phosphorylated, and that ANP‐induced homologous desensitization of GC‐A correlates with receptor dephosphorylation, a mechanism which might contribute to a loss of function in vivo. In this study, tandem MS analysis of the GC‐A receptor, expressed in the human embryonic kidney cell line HEK293, revealed unambiguously that the intracellular domain of the receptor is phosphorylated at multiple residues: Ser487, Ser497, Thr500, Ser502, Ser506, Ser510 and Thr513. MS quantification based on multiple reaction monitoring demonstrated that ANP‐provoked desensitization was accompanied by a complex pattern of receptor phosphorylation and dephosphorylation. The population of completely phosphorylated GC‐A was diminished. However, intriguingly, the phosphorylation of GC‐A at Ser487 was selectively enhanced after exposure to ANP. The functional relevance of this observation was analysed by site‐directed mutagenesis. The substitution of Ser487 by glutamate (which mimics phosphorylation) blunted the activation of the GC‐A receptor by ANP, but prevented further desensitization. Our data corroborate previous studies suggesting that the responsiveness of GC‐A to ANP is regulated by phosphorylation. However, in addition to the dephosphorylation of the previously postulated sites (Ser497, Thr500, Ser502, Ser506, Ser510), homologous desensitization seems to involve the phosphorylation of GC‐A at Ser487, a newly identified site of phosphorylation. The identification and further characterization of the specific mechanisms involved in the downregulation of GC‐A responsiveness to ANP may have important pathophysiological implications.Structured digital abstract MINT‐7713870, MINT‐7713887: PMCA (uniprotkb:P20020) and GC‐A (uniprotkb:P18910) colocalize (MI:0403) by fluorescence microscopy (MI:0416)