Optimizing the use of organic and mineral fertilizer in rain-fed maize production is crucial for sustainable food production in sub-Saharan Africa. This study investigates the effect of hill-placement of two nutrient sources (farmyard manure and synthetic fertilizer) on nutrient- and water-use efficiencies of maize crops i.e. recovery efficiency (NUEre), internal utilization efficiency (NUEie) and water use efficiency (WUE). A four-year trial was conducted in the tropical sub-humid zone of the northern Benin with a factorial combination of farmyard manure at three levels (0, 3 and 6 t ha−1, hereafter NM, 3M and 6M, respectively) and three levels of fertilizer [0% (NF), 50% (50F) and 100% (100F) of the recommended rate (76 kg N + 13.1 kg P + 24.9 kg K ha−1) by the national center for agricultural research. The NUEre decreased with increasing rate of manure and/or fertilizer, but the decreasing rate was lower under combined manure and fertilizer application. However, the NUEie increased with the increasing manure and fertilizer amounts. The WUE was significantly higher in 3M and 6M treatments than in NM treatment, and higher in 50F and in 100F than in NF treatments. The combination of 3000 kg ha−1 farmyard manure with half recommended fertilizer rate (100 kg ha−1) could be suggested as an optimal nutrient management practice for maize production in the Northern Benin. Future studies should target the other agro-ecological zones in Benin, and also consider other widely cultivated crops in the study area for reducing yield gaps and promote food security.