The Plasmodium falciparum chloroquine resistance transporter (PfCRT) is a key contributor to multidrug resistance and is also essential for the survival of the malaria parasite, yet its natural function remains unresolved. We investigated the native substrates of PfCRT in both the Xenopus oocyte expression system and isogenic parasite lines expressing different pfcrt isoforms, using complementary physiological, biochemical, and metabolomic approaches. We identify host-derived peptides of 4-11 residues, varying in both charge and composition, as the substrates of PfCRT in vitro and in situ, and show that the protein does not mediate the non-specific transport of ions and other metabolites. We found that drug-resistance- conferring mutations reduce both the peptide transport capacity and substrate range of PfCRT, explaining the impaired fitness of drug-resistant parasites. The transport of peptides and peptide mimics via PfCRT is saturable and inhibited by verapamil and quinoline drugs. Our results indicate that PfCRT transports peptides from the lumen of the parasite’s digestive vacuole to the cytosol, thereby providing a source of amino acids for parasite metabolism and preventing osmotic stress of this organelle. The long-awaited resolution of PfCRT’s substrate-specificity and physiological role will aid the development of drugs that target PfCRT and/or restore the efficacy of existing antimalarials.