Micro-organismal interspecies competition induces highly complex ecological interactions. Its associated biochemistry is an extremely rich source for bioactive molecules, that can be evaluated by comparing assays of separated species to ‘co-cultures’ in which they compete. The untargeted view that metabolomics provides, gives unprecedented insight into the wealth of involved metabolites. Currently used multivariate data analysis methods in metabolomics, like principal component analysis, do not focus upon up- and down-regulation of constitutive metabolite pools during competition. This severely limits the interpretation of competition mechanisms and the associated metabolites from the extremely information-rich metabolomics data. Projected orthogonal chemical encounter monitoring (POCHEMON) is a novel multivariate data analysis method that reveals all competition-related biochemical changes from the co-cultures: both up- or down-regulated, and de novo synthesised metabolites. It describes the metabolite composition of a co-culture assay by a mixture of the metabolites expressed in both separated species. Aspects of the co-culture metabolism that cannot be described in this way, are present only in the co-cultures and therefore likely associated to interspecies competition. We highlight the potential of POCHEMON by a study on fungal interactions in onychomycosis, a nail infection that may severely affect immuno-suppressed individuals. The resulting model reveals many unexpected or as yet unknown metabolites involved in the competition, that can be specifically identified as up- or down-regulated or de novo produced upon competition.