In this study, the separation of four neuromedin-like peptides is investigated on four different core-shell stationary phases. Moreover, the effect of the mobile phase composition, i.e. organic modifier (acetonitrile and methanol) and additive (trifluoroacetic acid, formic acid, acetic acid, ammonium formate and ammonium acetate) on the chromatographic performance is studied. An improvement in chromatographic performance is observed when using the ammonium salt instead of its corresponding acid as additive, except for the column containing a positively charged surface (C18+). In general, the RP-Amide column provided the highest separation power with different mobile phases. However, for the neuromedin-like peptides of interest, the C18+ column in combination with a mobile phase containing methanol as organic modifier and acetic acid as additive provided narrower and higher peaks. A three-factor, three-level design is applied to further optimize the method in terms of increased peak height and reduced solvent consumption, without loss in resolution. The optimized method was subsequently used to assess the in vitro microdialysis recovery of the peptides of interest. Recovery values between 4 and 8% were obtained using a perfusion flow rate of 2 μL/min.