Use of inorganic fertilizers in smallholder cropping systems in Africa is often becoming inefficient due to increasing unresponsiveness to fertilizer application. A study was conducted for 2 years (four seasons) to assess the effects of biochar made from Prosopis juliflora (Sw.) DC. biomass on nutrients, fauna abundance and subsequent influence on maize planted in a nitisol. There were 12 amendments comprising: (i) biochar applied alone at a rate of 5 and 10 Mg ha−1; (ii) three fertilizer types applied separately (di-ammonium phosphate (18:46:0), urea (46:0:0) and composite NPK (23:23:0)); (iii) six fertilizer + biochar blends of the three fertilizer types and two biochar rates (0.05 and 0.1 Mg ha−1); and (iv) a control with no inputs. Treatments were replicated four times in a randomized complete block design. The amendments were applied in the first two seasons, while the last two were used to assess residual effects. At the end of the first two seasons, total C and N were higher in soils where biochar or fertilizer + biochar was applied, with more than 15.0 g C and 1.9 g N kg−1, compared to 10.4 g C and 1.0 g N kg−1 in control plots. Available P and exchangeable K were over 200% and 100% higher in biochar or fertilizer + biochar amended than control soils, respectively. Application of biochar had no effects on macrofauna such as beetles, centipedes, millipedes, termites and ants, but attracted earthworms. Soil that received 10 Mg biochar ha−1 recorded twice the number of earthworms (207 individuals m−2) compared to soil with 5 Mg biochar ha−1 (105 individuals m−2) and control (97 individuals m−2). Soils which received biochar, with or without fertilizer, had higher taxonomic richness (7.0 species) compared to soils which received DAP (2.8) or NPK (3.8). Nematodes, particularly bacterivorous groups, decreased by more than eight times with biochar application. In the first and second seasons, 5.6 Mg maize grain yield ha−1 was obtained from plots amended with biochar (without fertilizer), which was about six times higher than that harvested from unfertilised control at 0.9 Mg ha−1. Yield differences in plots where fertilizer was applied with or without biochar were not significant. Yield in the third and fourth seasons declined to 3.2 and 1.5 Mg ha−1, irrespective of fertilizer type or biochar amounts.