Total ecosystem carbon storage has frequently been found to increase with woody encroachment in savannas. However the loss of grass roots associated with woody encroachment can lead to a decrease in below-ground carbon storage which is not compensated for by an increase in above-ground carbon. To investigate how the extent of total woody cover affected ecosystem carbon, soil and above-ground carbon storage along eight thicket–savanna and five forest–grassland boundaries were measured. To investigate whether changes in soil carbon concentrations were related to the percentage of C4 (grass) roots to total roots and root quantity and quality, we measured fine-root biomass, root C : N ratios, root N, and % C4 roots at three different depths across thicket patches of different ages (n = 189). Forests contained significantly more carbon than adjacent grasslands in both above-ground carbon (mean difference 12.1 kg m−2) and in the top 100 cm of the soil (mean difference 4.54 kg m−2). Thickets contained significantly more above-ground carbon than adjacent savannas (3.33 kg m−2) but no significant differences in soil carbon were evident. Total fine-root biomass appeared to be more important than root quality (root C : N) in determining soil carbon concentrations during the encroachment process (i.e. in thicket of different ages). Similarly for thickets, the % C4 roots had no significant effect on soil carbon concentrations. In conclusion, thicket invading into open savanna vegetation did not lead to significant gains in ecosystem carbon at this study site. Significant gains were only evident in mature forest, suggesting that the process may take place very slowly.