The stereoisomers of N‐phthaloyl‐protected amino acids and dipeptidomimetics were separated on macrocyclic glycopeptide and cellulose‐based chiral stationary phases (CSPs) in the RP and polar‐ionic modes. The effects of the organic modifier, the mobile phase composition, and the pH on the separations were investigated. Optimization of these separations was achieved through variation of the mobile‐phase additive combinations. The elution sequence was determined for some of the samples. A practical application for the monitoring of the reaction conditions for N‐phthaloylation of (S)‐Phe was demonstrated.