Protein phosphorylation is a critical and ubiquitous post-translational modification (PTM) found across the kingdoms of life. Advances in high-throughput mass spectrometry have transformed our ability to interrogate the phosphoproteome. However, sample prepara-tion methodologies optimized for phosphoproteomics have not kept pace, compromising the ability to fully exploit these technological capabil-ities. In this study, we present an optimized phosphoproteomics workflow using carboxylated SP3 magnetic beads which have revolutionized proteomics sample preparation. By employing a washing step with 8 M urea and omitting the conventional C18 SPE clean-up, we demon-strate a significant improvement in phosphopeptide identifications, with application of this refined protocol to HEK-293T cell extracts increas-ing the number nearly 2-fold compared to standard SP3 techniques. We also observed a substantial improvement in the detection of multiply phosphorylated peptides. Our findings suggest that the complexity of PTM crosstalk using current peptide-based proteomics workflows is currently underexplored, and underscores the necessity of methodological innovations to better capture the intricacies of the phosphoproteome landscape.