Soil microbial communities are known to dominate most biogeochemical processes. These processes—and thus the diversity and composition of the microbial communities that drive them—are essential for the functioning of ecosystems, both in natural and managed, agricultural settings. Efforts to feed growing human populations have led to the extension of organic and mineral fertilizers in previously unused quantities. Little is known about the impacts of these efforts to increase food production on ecosystems. Particularly little is known about their impacts on soil microbial communities, which dominate most biogeochemical processes; even less is known about their impacts in the tropics, where most smallholder farmers reside. We collected soil from experimental plots and actively managed farms in western Kenya to assess the impact of agricultural intensification on soil microbial communities in sub-Saharan Africa. We find that the taxonomic diversity of soil microbial communities is impacted by fertilizer applications in experimental plots, but that these taxonomic differences do not correspond with changes in functional capacity. The addition of C through improved fallows has an impact on the functional capacity of microorganisms. Our results suggest that although most nutrient addition studies with microbes have been done with N-based fertilizers, the availability of C--mediated through plant functional triats--may be more important in determining the functional diversity of belowground communities. These results further imply that efforts to increase crop yields for smallholder farmers can enhance microbial diversity and functioning in the presence of land-sharing strategies, such as agroforestry.