Synthetic phosphopeptides are frequently used as chemical probes to explore protein–protein interactions involved in cellular signal transduction. Most commonly, the solid-phase synthesis of phosphotyrosine-containing peptides is performed by applying the Fmoc-strategy and N-Fmoc-protected tyrosine derivatives bearing acid-labile phospho protecting groups. We observed a side-reaction, the isomerisation at threonine, which furnishes depsipeptides. It is shown that the rate of N→O-acyl migration depends on the sequence context. Depsipeptides were formed most rapidly when the phosphotyrosine was located in the +2 position. Furthermore, different phosphotyrosine building blocks were compared and a suitable method that provides phosphopeptides in enhanced purity and yield is suggested.