Long-term effects of integrated soil fertility management practices on soil chemical properties in the Sahel

•ISFM treatments increased long-term grain yields by 1.4–8.7 times in Sahel.•Cereal-legume rotation had higher average yields compared to the continuous cropping.•Manure addition at 40,000 kg ha−1 prevented fertilizer induced acidification.•Microbially-derived N moieties increased with organic inputs as indicated by XANES.•Manure addition at 40,000 kg ha−1 led to the increase in soil C, N and P levels.