The growing exploitation of natural resources is increasing the human-induced pressure on soil. Industrial, metallurgical, and mining operations release excessive amounts of heavy metals into the soil. Waste and wastewater from various facilities also contribute to contamination. These metals accumulate in the soil and can disrupt the bacterial community, which is an essential indicator of soil health. Modern molecular genetic tools, such as shotgun sequencing and met barcoding of standard DNA markers are widely used to study soil bacterial diversity. This review summarizes recent research on how heavy metals affect soil bacterial communities using metagenomics approaches. Studies from the past decades consistently reveal that heavy metal pollution generally harms bacterial diversity and alters community structure. Several factors also influence metal toxicity, such as soil salinity, pH, ecosystem type, the presence of plant roots, and other soil characteristics. The paper further highlights potential future directions for research in this field.