AbstractSoil fertility depletion is a major constraint to agricultural production for smallholder farming households in many sub‐Saharan countries, and it is worsened by climate variability. In order to sustain food security for a growing population, measures have to be taken against C and nutrient losses from soils. This study examines whether banana–coffee agroforestry systems can improve soil fertility and C pools in smallholder farms in E Africa amidst observed climate variability. We selected 20 farms in Central Uganda, where soil samples were obtained from the top and subsoil layers. Samples were analyzed for several soil fertility parameters including soil organic matter (SOM), total soil organic C, pH, total N, plant‐available P, exchangeable K, texture, and bulk density. Soil C stocks were calculated based on soil organic C concentrations and bulky density. We measured tree diameter and height and calculated aboveground plant biomass using allometric equations. Belowground biomass was estimated using equations based on the respective aboveground plant biomass. Our results show that banana–coffee agroforestry farming systems had significantly higher total SOM and total N compared to the banana monoculture. Similar trends were observed for soil C stocks and total C pools. The former contained 1.5 times higher soil C stocks than the latter. Likewise, the mean total C pools for the banana–coffee agroforestry farm plots were 26% larger than that under banana monoculture. However, exchangeable K was higher in the soil of banana monocultures. Plant‐available P levels were limiting under both farming systems. The study demonstrates that beyond socio‐economic benefits banana–coffee agroforestry farming systems have beneficial effects on soil fertility and C sequestration compared to banana monocultures in the study area. However, precautions to avoid P depletion have to be taken under current climate conditions.