The malaria parasite Plasmodium falciparum possesses a ‘plastid-like’ organelle called an apicoplast. The apicoplast's prokaryotic-like translation apparatus is the target of several clinically-used antimalarials. Parasites treated with these drugs can replicate and invade a new host red blood cell before arresting in their second infection cycle, a characteristic known as the ‘delayed death’ effect. Treated parasites fail to transmit a functional apicoplast to their daughter cells, which are thus depleted of the apicoplast’s sole essential metabolic product: isopentenyl pyrophosphate (IPP). IPP is the principle isoprenoid precursor, and isoprenoid compounds are presumed to be required for protein-prenylation, the formation of dolichol-lipid-carriers, and the generation of the electron-carrier ubiquinone in mitochondria. However, it remains unclear what consequences isoprenoid depletion has on parasite cellular processes and how they contribute to parasite delayed death. We have investigated the metabolic fate and essentiality of isoprenoid compounds produced by the apicoplast and characterised the molecular and morphological phenotype of delayed death. Metabolomic analysis together with fluorescence uptake experiments suggest that there is a disruption in digestive vacuole (DV) function and morphology in parasites undergoing delayed death. This is further supported by our analysis using serial block-face scanning electron microscopy, which shows that the DV fragments into multiple compartments in delayed death parasites and that these parasites also have an abnormal phagosome network. We hypothesise that these phenomena arise from a defect in endosome trafficking to the DV due to aberrant prenylation of vesicular trafficking proteins. Supplementing delayed death parasites with the precursor for protein prenylation fully reverses the abnormal DV phenotype and temporarily rescues parasites for an additional infection cycle in proliferation assays. This suggests that interruption of protein prenylation, and consequent cellular trafficking defects, are proximal causes of delayed death and therefore reveals the mode of action for these important drugs.