Allelopathy contributes to interspecific interference in plants beyond competition for nutrients and sunlight and is of interest in agriculture due to its potential use in weed suppression. In order to study allelopathic effects in a model system, Arabidopsis thaliana and Trifolium repens were co-cultivated on nutrient medium in sterile containers for two weeks and then harvested, extracted and analyzed by GC-TOF-MS. 163 metabolites were identified using the automated database BinBase. Comparing metabolite peak areas in co-cultivated and control seedlings revealed an altered metabolic profile for both species in terms of several metabolite groups including amino acids, phenolics, carbohydrates and lipids. 87 A. thaliana and 53 T. repens metabolites were significantly affected. In A. thaliana 34 metabolites increased relative to the control upon co-cultivation while 54 decreased; in T. repens 20 increased while 33 decreased. To our knowledge, this is the first plant-plant interaction study making use of untargeted library-based metabolomics. The observed decreases in A. thaliana of aromatic and branched-chain amino acids suggest a suppressant effect of T. repens on A. thaliana which may resemble that of herbicides, as the synthesis of these two groups of amino acids is inhibited by glyphosate and sulfonylurea herbicides respectively. While the results are not conclusive, they illustrate the power of untargeted library-based metabolomics in descriptive studies and in generating hypotheses for further study.