African tropical forests are thought to play an important role in global carbon sequestration. However, the increasing rate of deforestation and the impact of changes in land use require a critical and updated look at what is happening. This work emphasizes the role of bulk density as a main driver in carbon (C) and nitrogen (N) stock in four land-use categories: natural forest, tree plantations, crop land and degraded soil. The study was conducted in the Central Highlands of Ethiopia, where deforestation and human pressure on native forests are exacerbated and erosion has caused extensive soil loss. The methodological approach consisted of evaluating the confounding effect of bulk density and then estimating C and N stocks based on a fixed-mass method rather than the usual fixed-depth method, in order to compare differences across land use categories. We hypothesized that elevation gradient would play a determining role in C and N concentrations and stocks in native forest, whereas tree species would be the main factor in plantations. C and N concentrations and bulk densities in mineral soil were analyzed as repeated measures in an irregular vertical space ranging from 0–10 cm, 10–30 cm, 30–50 cm and 50–100 cm, using a linear mixed model approach. Single observations from the forest floor were analyzed by a general linear model. Results indicated that soil depth is a more important factor than elevation gradient in native forests, though C and N concentrations and stocks diminished near human settlements. Native forest stored on average 84.4%, 26.4% and 33.7% more carbon and 82.4%, 51.8% and 27.1% more nitrogen than bare soil, crop land and plantations, respectively. Conversion of crop and degraded land to plantations ameliorated soil degradation conditions, but species selection did not affect carbon and nitrogen stocks.