The capacity for soils to serve as a carbon (C) reservoir is dependent on the persistence of soil organic carbon (SOC). Interactions between organic and mineral phases in soil are a key component of long-term SOC persistence, but the small spatial scale at which they occur makes direct observation of interaction mechanisms challenging. In this work, we used cryogenic scanning transmission electron microscopy with electron energy loss spectroscopy (cryo-STEM-EELS) to image and chemically characterize organo-mineral and organo-organic interfaces in a natural soil sample. This dataset includes cryo-STEM-EELS point, line, and 2D map measurements, as well as additional characterization data from electron dispersive X-ray (EDX) spectroscopy. Statistical analysis of cryo-STEM-EELS data and figure source data are also included. This study revealed a patchy distribution of organic forms, rather than previously observed organized layers at mineral surfaces. We detected enrichment of nitrogen (N) at both organo-mineral and organo-organic interfaces, but different forms of C, with oxidized C or alkyl C enriched at organo-mineral or organo-organic interfaces, respectively. This study supports a new view of SOC spatial architecture at mineral surfaces, and provides motivation to evaluate how organic N composition of organic inputs may affect long-term SOC persistence.