The selectivity for 15 biogenic amines and amino acids shown by three capillary cation-exchange columns, IonPac CS19, CS12A and CS17 (250 × 0.4 mm ID, all from Thermo Fisher Scientific), exhibiting medium, medium low and ultra-low hydrophobicity, and either carboxylic or mixed carboxylic/phosphonic acid functional groups, was investigated. A mixed mode retention mechanism was revealed with ion-exchange, hydrophobic and hydrogen bonding interactions contributing to retention of polar organic molecules on these phases. The relative impact of these interactions was evaluated via the effect of concentration and pH of the eluent (methanesulfonic acid) on the retention of fifteen structurally similar biogenic amines and amino acids. Strong hydrogen bonding interactions were observed between the solute amino acid carboxylic groups and cation-exchange groups from the ion-exchangers. This is the first time retention data correlated with logP data has revealed clustering of the solutes in two groups, according to the presence or absence of a carboxylic acid functional group. In addition, stronger retention behaviour was found for the IonPac CS12A cation-exchanger, containing both carboxylic and phosphonic functional groups. Further assessment of the orthogonality plots of retention factors for the three stationary phases revealed that the columns exhibited different complimentary selectivity that can be utilised to achieve specific separations.