Soil microbial biomass elements and mineralization processes are essential in replenishing soil nutrients. Yet, the effect of fertilization on the microbes is still not well-defined. This study aimed to determine the effect of integrated soil fertility inputs (inorganic and organic) on microbial biomass, carbon (MBC), nitrogen (MBN), phosphorus (MBP), nitrogen (N) mineralization, and N use efficiency in a field experiment. The treatments were: control (no fertility input), sole inorganic fertilizer, and different combinations of inorganic and organic inputs in a randomized block design. The results showed that Conventional tillage + maize residue + goat manure + Dolichos lablab intercrop (CT4); minimum tillage + maize residue + Tithonia diversifolia + goat manure (MT5); and minimum tillage + maize residue + goat manure + Dolichos lablab (MT4) intercrop increased microbial C, N, and P by 78 %, 48 %, and 41 %, respectively compared to control (CT0). Compared to CT0, N mineralization significantly varied (p < 0.0001) among the treatments at planting and on the 15th, 30th, 45th, and 60th days after planting during the 2020 short rains season. It also differed significantly (p = 0.0018, 0.0028, < 0.0001, and 0.0028,) on the 45th, 60th, 75th, 90th, and 105th days, respectively, relative to CT0 after planting during the 2021 long rains season. The CT4 had 5.11 and 52.80 kg N ha−1 higher apparent nitrogen recovery and partial factor productivity N, respectively. Similarly, MT4 greatly enhanced N apparent recovery efficiency by 57.5 % relative to CT0. Integrating fertility inputs improved soil biological fertility and mineralized N. Therefore, technologies that integrate organic inputs, either solely or with inorganic fertilizers, should be harnessed and promoted as medium and long-term technologies to advance soil biological fertility, and mineral N and N use efficiency in smallholder farmers.