The impact of industrialisation, urbanisation and unsafe agricultural practices has led to the introduction of heavy metals and organic pollutants into the soil. The presence of these contaminants threatens ecosystems, reduces soil quality and harms human health. This paper aimed to examine the efficacy, efficiency and cost-effectiveness of microbial bioremediation as a means of soil detoxification. Bioinformatics and genetic engineering are emphasised as key tools in the degradation of recalcitrant pollutants using microbial systems. The combination of computational biology and biotechnological tools can optimise bioremediation processes through innovative strategies. This study demonstrated that bioengineered microbes and microbial consortia play a significant role in ecological restoration and contamination reduction. Researchers have shown that microbial bioremediation has the potential to transform environmental remediation practices while enhancing sustainability and resilience.