AbstractProtein phosphorylation is one of the most studied post‐translational modifications (PTMs). Despite the remarkable advances in phosphoproteomics, a chemically less‐stable subset of the phosphosites, which we call the crypto‐phosphoproteome, has remained underexplored due to technological challenges. In this Viewpoint, we briefly summarize the current understanding of these elusive protein phosphorylations and identify the missing pieces for future studies.