Retention properties of 79 fungal metabolites (including neutral, acidic, basic, and amphoteric compounds) were evaluated on distinct mixed-mode reversed-phase/weak anion exchange (RP/WAX)-type stationary phases by liquid chromatography-electrospray ionisation-tandem mass spectrometry (LC-ESI-MS/MS) in gradient as well as in isocratic elution mode. The RP/WAX separation materials were prepared by functionalising thiol-modified silica with N-(10-undecenoyl)-3-aminoquinuclidine and N-(10-undecenoyl)-3-alpha-aminotropane, respectively. To evaluate complementarity in chromatographic selectivity the physico-chemically heterogeneous solute set was analysed also on a RP phase (C(18)), an amino-type WAX phase, and a commercially available RP/WAX-like mixed-mode phase. Analytes may interact with the RP/WAX ligands via (attractive/repulsive) ionic, RP-like hydrophobic, as well as hydrophilic (HILIC) retention mechanisms. Individual interactive increments were found to be basically controlled by the nature and amount of organic modifier, pH value of eluent, and ionic strength of buffer additives. It could be demonstrated that RP/WAX columns offer the potential to separate compounds by exploiting a combination of various chromatographic interaction modes, which is not accessible with conventional RP and WAX columns. Such multi-modal properties increase both versatility and degrees of freedom for adjustment of chromatographic selectivity. For example, highly polar mycotoxins such as moniliformin were well retained on RP/WAX-type phases without compromising RP-selectivity for neutral (e.g. aflatoxins) and most basic solutes (e.g. epimer separation of ergot alkaloids) under fully MS-compatible conditions like a hydro-organic eluent with acetonitrile as organic modifier and an acetic acid/ammonium acetate buffer. Flexibility of the employed mixed-mode separation materials may be of value particularly for LC-ESI-MS/MS-based bioanalytics involving analytes with widely varying physico-chemical properties or applications prone to matrix effects.