Heavy metal contamination of soil around mining sites is a serious environmental issue. The soil microbial-driven nitrogen (N) mineralization was inhibited by lead (Pb) contamination, which reduces agricultural productivity. To recover the contaminated soils’ microbial processes, organic amendments such as chicken manure (CM) have been usually adopted. Besides, managing animals on soils provides fresh organic matter and accelerates N cycle thus it might recover the inhibited process in Pb contaminated soils. However, the effects of CM and animals on the microbiome and N cycle in the Pb contaminated soils were still unclear. Here, we used mice and CM as amendments for Pb contaminated soils to investigate their effects on the N mineralization and its relevant microbiome. Pb pollution decreased the nitrification rate as expected. The CM increased the nitrification rate which was lowered by the Pb pollution through the increase in ammonia-oxidizing archaea and bacteria, while the presence of mice itself did not. Without the CM, the mice relatively increased the abundance of the ammonia oxidizers, but their disturbing effect (e.g, drying soils) might decrease the ammonia oxidizer’s activities. Overall, we need to consider both positive and negative effects of CM and mice for application in Pb contaminated soils.