Variations in the carbon isotopic composition of soil organic matter (SOM) in bulk and fractionated samples were used to assess the influence of C3 and C4 vegetation on SOM dynamics in semi-natural tropical ecosystems sampled along a precipitation gradient in West Africa. Differential patterns in SOM dynamics in C3/C4 mixed ecosystems occurred at various spatial scales. Relative changes in C / N ratios between two contrasting SOM fractions were used to evaluate potential site-scale differences in SOM dynamics between C3- and C4-dominated locations. These differences were strongly controlled by soil texture across the precipitation gradient, with a function driven by bulk δ13C and sand content explaining 0.63 of the observed variability. The variation of δ13C with soil depth indicated a greater accumulation of C3-derived carbon with increasing precipitation, with this trend also being strongly dependant on soil characteristics. The influence of vegetation thickening on SOM dynamics was also assessed in two adjacent, but structurally contrasting, transitional ecosystems occurring on comparable soils to minimise the confounding effects posed by climatic and edaphic factors. Radiocarbon analyses of sand-size aggregates yielded relatively short mean residence times (τ) even in deep soil layers, while the most stable SOM fraction associated with silt and clay exhibited shorter τ in the savanna woodland than in the neighbouring forest stand. These results, together with the vertical variation observed in δ13C values, strongly suggest that both ecosystems are undergoing a rapid transition towards denser closed canopy formations. However, vegetation thickening varied in intensity at each site and exerted contrasting effects on SOM dynamics. This study shows that the interdependence between biotic and abiotic factors ultimately determine whether SOM dynamics of C3- and C4-derived vegetation are at variance in ecosystems where both vegetation types coexist. The results highlight the far-reaching implications that vegetation thickening may have for the stability of deep SOM.