Lime is used to reduce soil acidification in agricultural soils. However, its effects on microbial diversity, stability and abundance is not clear. Therefore, an incubation experiment was set up to determine the effect of soil pH (6.5-Lime-L and 5.5-No Lime-NL) and fertilizer (anaerobic digestate-AD and urea-U) on inorganic nitrogen and microbial properties. Soils were sampled once a week to monitor changes in chemical, microbial and gene (16S, AOA, AOB and nosZ) abundance. In results, beta diversity (unifrac) showed that samples from the same pH and fertilizer shared a high degree of similarity. The impact of AD on soil microbes varied based on pH. In NL treatments AD had a significant effect on more (165) microbes compared to L (140), indicating that microbes were more stable in L. Soil pH and fertilizer had a significant effect on 16S with highest values observed in L and AD. Soil pH and fertilizer had a significant effect on AOA with highest values recorded in L and U. In L, highest AOB numbers were observed in AD, and in NL, highest numbers were in U treatments. The results indicate that lime application positively modulates soil microbial diversity, stability and abundance in agricultural soils.