Electrochemical degradation of lignin results in a large number of unknown products, formed by both oxidative and reductive decomposition pathways, which have previously been studied by direct mass spectrometry experiments without prior liquid chromatography separation, revealing the presence of many isobaric molecules. In this study, novel phosphonium‐based ionic liquid stationary phases were synthesized and applied in conjunction with high resolution mass spectrometry, to further increase the resolving power of the analytical methodology. The new stationary phases exhibited a wide range of interaction mechanisms in comparison to reversed‐phase materials, and the preliminary results of this proof‐of‐concept study illustrated class‐specific isolation and separation of the major chemical classes of the lignin breakdown products members into very specific retention time windows. For the investigated electrochemically decomposed lignin, the separations revealed predominantly aldehydes and alcohols, and also confirmed the presence of a significant number of isobars.