This project contains quantitative proteomic data comparing native exosomes and mechano-exosomes derived from human adipose-derived mesenchymal stem cells. Cells in both groups were treated with Art-myosin; the mechano-exosome group was additionally subjected to periodic magnetic actuation at 12-h intervals over 48 h, whereas the native-exosome group was maintained without magnetic actuation. Exosomes were isolated from conditioned medium by ultracentrifugation and analysed by LC–MS/MS in three biological replicates per group to characterize magnetic-actuation-associated changes in exosomal protein cargo.