Dataset description Interfaces between molecular and metallic layers have great potential for nanoscale quantum devices, sensors and novel magnetism. In our paper, “Emergent magnetism at transition-metal-nanocarbon interfaces” we describe the appearance of spin order in a variety of material combinations using fullerenes and RF sputtered carbon. The samples are measured via SQUID magnetometry, low energy muon spin spectroscopy and X-ray magnetic circular dichroism. In this work, we explore as well the effects that annealing, structural recombination and oxygen intercalation may have in this emergent magnetism. The results may have repercussions in the design of hybrid magnetic materials and multifunctional devices for electronics and spintronics. This dataset contains the raw data for the published figures and the collected measurements in beamtime experiments, as well as changes in magnetometry during the annealing process.