Access to large phenotypic screens has enabled the discovery of a number of compounds which can kill the malaria parasite in vitro. Translating these findings into new anti-malarial drugs faces a number of challenges. Finding the mode of action of these compounds can help in focussing efforts to develop the most promising compounds and help in designing new combination therapies targeting different pathways in the parasite to overcome drug-resistance. Using a microplate-based, untargeted metabolomics analysis of Plasmodium falciparum, we investigated the mode of action of 11 potent antimalarial compounds obtained from the Medicines for Malaria Venture and the Open Source Malaria project. This approach revealed significant metabolic perturbation associated with the most potent compounds, and identified the most likely pathways targeted by each compound. The major metabolic pathway intermediates which were found to be perturbed were from the pyrimidine biosynthesis pathway, glycolysis, phospholipid metabolism and haemoglobin degradation. Multivariate analyses allowed classification of some novel compounds that targeted the same biochemical pathways as two known anti-malarials, Atovaquone and Cipargamin. Interestingly, compounds showing similar biochemical activities did not always have similar chemical structures.  This study shows that a simple and efficient metabolomics assay can rapidly reveal the biochemical basis of the mode of action of newly discovered anti-malarials. This information can be used for prioritising compounds before progressing them through the optimization pipeline and further development.