To enhance the repertoire of molecular tools for studying malaria parasite biology, we adapted a ligand-regulatable FKBP protein destabilization domain (ddFKBP) for use in P. falciparum. We destabilized the reporter yellow fluorescent protein (YFP) and the P. falciparum protease falcipain-2 in a ligand-reversible manner by tagging with ddFKBP. The swollen food vacuole phenotype of falcipain-2 knockout parasites could be rescued in a Shld1 ligand-dependent fashion by falcipain-2-ddFKBP expression.