Inefficient fertilizer management and increasing water scarcity are affecting rice yields and thus food security in Central African lowlands. The objective of the study was to determine the effect of biochar and mineral fertilizer application and irrigation regime on paddy rice growth, yield and profitability. A randomized complete block design with a split‐split plot arrangement and three replications was used at three field sites and for two consecutive seasons. The main plots consisted of two irrigation regimes, permanent flooding and alternate wetting and drying. Rice (Oryza sativa L.) cultivars TAI and AR2017105 were assigned to subplots. Six fertilization treatments were applied in sub‐subplots: control, rice husk biochar or manure‐charged biochar, each with and without mineral fertilizer. Alternate wetting and drying did not penalize yield. The combined use of biochar and mineral fertilizer increased paddy rice yield compared to fertilizer alone (+16%) and the control (+85%). The sole application of biochar, with or without manure, did increase yield in the first (+14%) but not in the second season compared to the unfertilized control. In both cropping seasons, the combined use of biochar and mineral fertilizer significantly increased the gross margin of paddy rice farming compared to the sole application of fertilizer. The combined application of biochar and mineral fertilizer under alternate wetting and drying can thus be recommended as a key climate‐smart agricultural practice to increase food security and the agronomic profitability of rice cropping in Central African lowlands and comparable rice growing areas worldwide.