This dataset contains a hyperLOPIT spatial proteomics experiment performed on Plasmodium falciparum to determine the subcellular localization of parasite proteins. Schizont-stage parasites were fractionated by density gradient centrifugation, and collected fractions were labelled with tandem mass tags (TMT) for multiplexed quantification. Peptides were analysed by LC–MS/MS on an Orbitrap Fusion Lumos mass spectrometer. Protein identification and quantification were performed using Proteome Discoverer with the Sequest HT search engine against the P. falciparum reference proteome and human proteome. The dataset supports high-resolution mapping of organelle localization and contributes to understanding the compartmental organization of the malaria parasite proteome.