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Lack of data on carbon stocks hampers implementation of emission reduction mechanisms (e.g., REDD+). Addressing this issue is relevant, especially when combined with other challenges such as preserving biodiversity. The present study assessed tree diversity (Shannon–Wiener’s index) and carbon stocks of different land uses in Balé and Ziro sites in Sudanian zone of Burkina Faso. Aboveground carbon stock was evaluated using generalized equation. Belowground carbon was assessed by excavating plant parts in samples of soil in each plot. Regarding soil sampling for C-content assessment, four locations were selected in each plot and soil was sampled at the depths of 0–20 cm and 20–50 cm, using an auger. The four soil samples from each depth were pooled, thoroughly mixed and a composite soil sample taken to the laboratory for carbon content measurement using the Black and Walkley method. The C-content was then used for calculating SOC. In Balé and Ziro, 85 and 106 species, 63 and 82 genera, 29 and 35 families were identified, respectively, with the Leguminosae family as most dominant. Natural vegetation stands (NV) and fallows showed high richness and diversity compared to parklands. Soil was found the most important carbon pool. Highest values of aboveground, belowground and soil C-stocks in Ziro (13.9, 14.71 and 67.1 Mg/ha) were recorded in community managed forests (CMF) logged 12 years ago, while equivalent values for Balé (25.76, 14.96 and 53.02 Mg/ha) were recorded in the dense NV. However, irrespective of C pool, the difference between CMFs and the 100 trees/ha Vitellaria parkland was not significant. Correlations were found between species richness and above and belowground C-stocks (R2 = 0.22, p < 0.0001; R2 = 0.33, p < 0.0001). Overall, dense Vitellaria parklands, apart from allowing tree-crop integration, have real potentials for C sequestration. Also, C-sequestration and biodiversity conservation are likely not conflicting targets.