Due to its recalcitrance against microbial degradation, biochar is very stable in soil compared to other organic matter additions, making its application to soils a suitable approach for the build-up of soil organic carbon (SOC). The net effects of such biochar addition also depend on its interactions with existing organic matter in soils. A study was established to investigate how the status of pre-existing soil organic matter influences biochar stabilisation in soil in comparison to labile organic additions. Carbon loss was greater in the C-rich sites (C content 58.0 g C/kg) than C-poor soils (C content 21.0–24.0 g C/kg), regardless of the quality of the applied organic resource. Biochar-applied, C-rich soil showed greater C losses, by >0.5 kg/m².year, than biochar-applied C-poor soil, whereas the difference was only 0.1 kg/m².year with Tithonia diversifolia green manure. Biochar application reduced the rate of CO₂-C loss by 27%, and T. diversifolia increased CO₂-C losses by 22% in the C-poor soils. With biochar application, a greater proportion of C (6.8 times) was found in the intra-aggregate fraction per unit C respired than with green manure, indicating a more efficient stabilisation in addition to the chemical recalcitrance of biochar. In SOC-poor soils, biochar application enriched aromatic-C, carboxyl-C, and traces of ketones and esters mainly in unprotected organic matter and within aggregates, as determined by Fourier-transform infrared spectroscopy. In contrast, additions of T. diversifolia biomass enriched conjugated carbonyl-C such as ketones and quinones, as well as CH deformations of aliphatic-C mainly in the intra-aggregate fraction. The data indicate that not only the stability but also the stabilisation of biochar exceeds that of a labile organic matter addition such as green manure.