Much effort has been spent on formulating guidelines for inorganic fertilizer use in millet crops in Sub-sahelian farms. However, these guidelines do not take into account the diversity of manuring practices. In this study we analyzed over two years (2016–2017) the use efficiency of an inorganic NPK fertilizer as affected by the two most contrasted categories of organic manure strategies (OMS) found in millet fields of central Senegal. 19 farmers’ fields were selected in a village typical of that region, 11 and 8 of which respectively corresponding to categories OMS1 and OMS2 as follows: OMS1, locally referred to as Homefields, were fields continuously cropped with millet over the last 15 years, having received organic manure regularly in the past, and manured again at the onset of the 2016 rainy season. OMS2 fields locally referred to as Outfields, were not manured in 2016 and were rarely manured in the past. Four of them were continuously cropped with millet and the others had followed a triennial millet-peanut-fallow rotation. In 2017, no manure was applied in any of the OMS1 or OMS2 fields. A pairwise treatments with and without the same inorganic fertilizer dose was applied in each field in both 2016 and 2017 cropping seasons. In 2016, the higher the manure application, the higher the use efficiency of the inorganic fertilizer applied. The use efficiency of the inorganic N was most closely related to soil bulk density and P availability. In 2017, with no new manure amendment, millet yield in OMS1 was about three times higher than in 2016. It was close to the water-limited yield, suggesting that the residual effect of the manure applied in 2016 was high. The use efficiency of the inorganic N was generally low under these conditions. In OMS2, millet yield and use efficiency of inorganic fertilizer remained low in both years. The crop rotation with peanuts did not enrich the soil compared to the millet returning every year, but it reduced Striga hermontica infestation and increased the millet 1000-grain weight. The methodological approach developed here may help in formulating guidelines to deal with the diversity of farming practices in Sub-sahelian villages.