Soils are not exempt from anthropogenic pollution, which can eventually cause disturbance of the microbial communities and areas without any kind of productivity. Among soil microbiota, bacteria play an important role in pollutant degradation, enabling them to thrive in contaminated sites. Given this, several techniques have been used to increase the number of pollutant-degrading bacteria in situ or for subsequent addition. Additionally, bacteriophages exhibit a high tolerance to pollutants and enhance bacterial metabolic activity through phage-encoded auxiliary metabolic genes (AMGs), thereby augmenting their skills for nutrient assimilation, resistance to phage infection, antibiotic resistance, heavy metal resistance, and degradation of pesticides and xenobiotics, among others. Several phage-encoded AMGs have been described during the last few years, but their diversity, distribution, and function have not been extensively explored, warranting further studies. Here, we highlight soil microbiome interactions, especially bacterium and phage interactions to understand this unexplored world with a high potential for restoring polluted soils.