Microdosing, the point-source application of a reduced fertilizer rate within 10 days of sowing, has increased short-term crop yields across the Sahel and is being actively scaled up as an agronomic practice. However, there is no information on the long-term effects of the technique upon soil fertility. To rectify this, this study used soil samples from the International Crop Research Institute for the Semi-Arid Tropics in Sadore, Niger, to assess the effects of 16 years of a reduced fertilizer rate of 15 kg N and 4.4 kg P ha−1 compared to unfertilized soil and a recommended rate of 30 kg N and 13.2 kg P ha−1 upon millet yield trend, soil chemical properties, and soil organic matter quality. The interaction of fertilizer with crop residue and manure amendments at 300, 900, and 2700 kg ha−1 was also assessed. Compared to unfertilized soil, the reduced fertilizer rate improved yield by 116 % but did not increase total N or available P. The recommended rate doubled available P and increased total N by 27 %, but resulted in slightly lower pH compared to the reduced rate. Yield trends were negative for both fertilizer treatments, indicating mineral fertilizer alone is not sustainable at Sadore. Crop residue or manure addition at 2700 kg ha−1 with fertilizer did not improve SOC but buffered pH by 0.3 units, provided nutrients beyond N and P, and changed the forms C and N functional groups in soil organic matter.