Pesticides are widely used in modern agriculture but exert significant pressure on soil microbial communities that sustain essential ecosystem functions. Evidence from both field experiments and meta-analyses indicates that pesticides alter microbial biomass, respiration, and enzyme activities, leading to long-term disruptions in soil functionality. Pesticide exposure has been reported to influence the structure and functioning of different soil microbial groups, leading to measurable changes in bacterial, fungal, and protist communities. These shifts, particularly under cumulative and multi-pesticide pressures, disrupt nutrient cycling and reduce the complexity of microbial interaction networks, ultimately weakening ecosystem resilience. The aim of this review is to provide an integrated evaluation of current studies addressing how pesticide exposure influences soil microbial communities and their functional interaction networks. Special attention is given to the potential of microbial diversity, functional activity, and network-level responses as bioindicators for ecosystem monitoring and sustainable agricultural practices. However, sustainable practices such as compost application, biofertilizers, and microbial consortia may help to restore microbial diversity and activity. Advances in molecular and omics-based tools further strengthen the use of soil microbiota as bioindicators, offering valuable insights for sustainable agriculture and ecosystem monitoring [21].