Co-amorphous systems have been shown to be a potential approach to address the poor water solubility challenge of many drugs. Various low molecular weight molecules, especially amino acids, have been used as potential co-formers. In this study, the differences between various combinations of amino acid-based systems, i.e. the single amino acids glutamic acid (Glu) and arginine (Arg), their physical mixture, glutamic acid-arginine crystalline and amorphous salts, and the corresponding dipeptides (GluArg, ArgGlu), were investigated. Mebendazole (Meb) was used as the model drug. Pure Meb and Meb-co-former mixtures were ball milled to prepare the co-amorphous samples. The shortest amorphization time upon ball milling (30 min) was found for Meb mixtures with the dipeptides and the Glu.Arg amorphous salt. All other samples became amorphous upon milling for 90 min, except Meb-Glu, where Glu remained partially crystalline. Both, single-phase (Meb-Glu-Arg ternary mixtures) and two-phase amorphous systems (Meb-Arg, Meb-GluArg, Meb-ArgGlu) were obtained for different Meb-co-former mixtures after milling. Whilst all co-formers improved the dissolution rate of Meb in a similar fashion (dissolution rate increased by 3.5 to 5.7-fold with respect to crystalline Meb), the highest stability improvement was observed for Meb-dipeptide systems. Interestingly, even though being a two-phase amorphous system, dipeptides were superior to the other co-formers as they possessed higher physical stability.