Purpose: The objective of this study is to improve our understanding of soil organic matter (SOM) stability in Brazilian Cerrado, by interpreting soil properties at the ecosystem scale and elaborating on the interactions of biotic, climatic and edaphic controls. Methods: Three 2 m soil profiles with significantly different total organic carbon TOC content but located on the same geomorphological unit were studied for δ13C isotopic composition to connect tree-grass patterns to TOC content. To gain insight into soil carbon stability, C/N, δ13C and δ15N were analysed for functional organic matter (OM) pools: free particulate OM (POM), occluded POM, base-extractable OM, and mineral-associated OM. Results: Small but abrupt shifts of δ13C with depth reflected simultaneous changes in tree-grass vegetation patterns over the past 10,000 years in all three profiles. These temporal changes were superimposed on spatial differences as indicated by consistent differences in δ13C values between the profiles, reflecting that site-specific differences in tree-grass patterns persisted over the past 10,000 years. Profiles with a historically larger contribution from trees (as evidenced by lower δ13C) had increased charcoal contents. Downward movement of charcoal by intense bioturbation occurred faster in the OM-rich soils as suggested by 14C dating. Conclusion: We found that long-term carbon storage in Brazilian Cerrado soils was a conjunction of wildfires, bioturbation, and local edaphic controls on tree-grass composition. Soils with an OM-rich thick A-horizon had more trees, more charcoal, and a higher activity of soil macrofauna, which was related to local differences in soil water availability.