The formation of acid mine drainage (AMD), which results from the oxidation of sulfur minerals by air and water, can be accelerated by acidophilic and chemolithotrophic bacteria such as Acidithiobacillus ferrooxidans. Our previous study revealed that walnut shell powder and its phenolic component inhibit the growth of A. ferrooxidans. However, their inhibitory effect on AMD formation in the environment needs verification. We established a bioleaching system to test whether walnut shell powder and its phenolic component can limit AMD formation. Our results showed that lignin and cellulose isolated from walnut shell decreased metal ion concentrations through absorption, whereas the phenolic component increased pH by downregulating the expression of Fe2+-oxidizing genes and rus operon genes of A. ferrooxidans. Only walnut shell powder showed an excellent ability to curb AMD by binding metal ions and increasing the pH value. On probing deeper into the alteration of the bacterial community structure in the bioleaching system, we found that the bacterial community became more diverse-the amount of A. ferrooxidans decreased and that of some non-acidophilic bacteria increased. The bacterial community in samples treated with walnut shell powder or its phenolic component had low abundance in the pathways of metabolism and energy production, as determined by phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt). In other words, preponderant microbes, mainly A. ferrooxidans, lacked energy to grow well in the treated samples. Our findings provide a practical applicability of walnut shell powder to reduce leaching from a complex environmental community.