Biochars have been recognized as an important material to improve soil properties. In a number of studies their beneficial properties have been found to increase with residence time in soil and during the composting process. The beneficial properties have been correlated with surface functional groups resulting from the interactions between char particles, inorganic and organic matter in the soil and soil biota. These interactions result in the formation of organo-mineral phases on the internal and external surfaces of the biochar. A paucity of information exists, particularly from longer-term field trials, on organo-mineral phases present on both the internal and external surfaces of the biochar. To characterize the structure of, and interface between, the carbon and mineral phases, we examined biochars recovered from two field trials and after composting from different countries using high resolution scanning electron microscopy (SEM), atomic resolution transmission electron microscopy (TEM) and scanning TEM (STEM), energy electron loss spectroscopy (EELS) and energy dispersive X-ray spectroscopy (EDS) at resolutions of 1–20 nm. The work revealed the formation of porous agglomerates of different minerals/inorganic compounds bound together with organic compounds on the surfaces of the biochar. In some cases, these agglomerates were bound together to form organo-mineral associations. The analyses also showed that the organic compounds containing both N and C functional groups and mixed valence iron oxide nanoparticles are possibly interacting with the organic compounds. The analysis also showed the formation of pores at the interface of the carbon matrix and organo-mineral aggregates.