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Abstract Anthropogenic perturbations have profoundly modified the Earth's biogeochemical cycles, the most prominent of these changes being manifested by global carbon (C) cycling. We investigated long-term effects of human-induced land-use and land-cover changes from native tropical forest (Kenya) and subtropical grassland (South Africa) ecosystems to agriculture on the dynamics and structural composition of soil organic C (SOC) using elemental analysis and integrated 13C nuclear magnetic resonance (NMR), near-edge X-ray absorption fine structure (NEXAFS) and synchrotron-based Fourier transform infrared-attenuated total reflectance (Sr-FTIR-ATR) spectroscopy. Anthropogenic interventions led to the depletion of 76%, 86% and 67% of the total SOC; and 77%, 85% and 66% of the N concentrations from the surface soils of Nandi, Kakamega and the South African sites, respectively, over a period of up to 100 years. Significant proportions of the total SOC (46–73%) and N (37–73%) losses occurred during the first 4 years of conversion indicating that these forest- and grassland-derived soils contain large amounts of labile soil organic matter (SOM), potentially vulnerable to degradation upon human-induced land-use and land-cover changes. Anthropogenic perturbations altered not only the C sink capacity of these soils, but also the functional group composition and dynamics of SOC with time, rendering structural composition of the resultant organic matter in the agricultural soils to be considerably different from the SOM under natural forest and grassland ecosystems. These molecular level compositional changes were manifested: (i) by the continued degradation of O-alkyl and acetal-C structures found in carbohydrate and holocellulose biomolecules, some labile aliphatic-C functionalities, (ii) by side-chain oxidation of phenylpropane units of lignin and (iii) by the continued aromatization and aliphatization of the humic fractions possibly through selective accumulation of recalcitrant H and C substituted aryl-C and aliphatic-C components such as (poly)-methylene units, respectively. These changes appeared as early as the fourth year after transition, and their intensity increased with duration of cultivation until a new quasi-equilibrium of SOC was approached at about 20 years after conversion. However, subtle but persistent changes in molecular structures of the resultant SOM continued long after (up to 100 years) a steady state for SOC was approached. These molecular level changes in the inherent structural composition of SOC may exert considerable influence on biogeochemical cycling of C and bioavailability of essential nutrients present in association with SOM, and may significantly affect the sustainability of agriculture as well as potentials of the soils to sequester C in these tropical and subtropical highland agroecosystems.