With soil degradation, the soils lose their carbon (C) and nitrogen (N), but questions remain whether the soils also lose their microbial ecosystem functions. The investigation of microbial structural changes due to the forest-to-farm conversion was needed as well as the prediction of their functions. We targeted sub-Saharan African soils because of the severeness of their degradation and the scarce information on the microbial properties. Soils were sampled from eight sites that had neighboring natural and farmed sites. After the measurement of soil properties, soil DNA was sequenced, targeting the 16S rRNA region. The soil prokaryotic community structures were checked and relative abundances of functional genes were estimated by the Tax4Fun package. On average, total C and N contents were decreased by the cultivation respectively. Unexpectedly, the Shannon diversity in farm soils was higher than that in natural soils despite the loss of prokaryotic abundance in most sites. Additionally, the relative abundances of several genes related to the N cycle and autotrophic C fixation were changed with the diversification. Overall, we might need to dissociate the story of microbial diversity from that of its abundance and nutritional richness, proposing a demand for clarification of the functional changes with the diversification.