Emerging resistance to artemisinins, and many currently used artemisinin partner drugs has necessitated the rapid development of new drugs with novel modes of action. We have used untargeted metabolomics to characterise the mode of action of new antimalarial drugs in development. Four drugs were investigated. Two current drugs (dihydroartemisinin and atovaquone) and two drugs in development; JPC-3210 (MMV 892646) and TSC-3. In vitro cultures of the P. falciparum strain, 3D7, were synchronised at 30 h after RBC invasion and exposed to 1 µM of drug in quadruplicate for 5 h. Parasite metabolites were subsequently extracted, separated by reverse phase chromatography and analysed on a high resolution orbitrap mass spectrometer. Data was processed and multivariate statistical analysis and biochemical pathway interpretation was performed using Ideom software and Metaboanalyst web-based tools. Over 700 putative metabolites were identified. Using principal component analysis (PCA, Metaboanalyst), we observe good clustering of the replicates from each of the 4 drug treatments. The two potent, new drugs JPC-3210, an aminomethylphenol, and TSC-3, a thiosemicarbazone, both cluster separately from the controls showing distinct metabolic profiles and suggesting novel modes of action. Comparison with six current antimalarials shows JPC-3210 clusters most closely with desethylamodiaqine and lumfantrine, two known hematin ploymerisation inhibitors. Examination of the JPC-3210 metabolic data shows defects in energy and lipid metabolism with many biochemical pathways perturbed. By contrast, TSC-3 shows a clear increase in the abundance of short peptides, many of which map to haemoglobin, suggesting the inhibition of one or more Plasmodium aminopeptidases. In conclusion, we have used high resolution mass spectrometry for untargeted metabolomics and have identified metabolic pathways involved in the modes of action of two potent, new antimalarial drugs in development. These findings also help direct future drug development for the treatment and eventual elimination of malaria.