This review summarizes the recent developments observed in the degradation of pesticide residues through biotransformation, chemical degradation, and photodegradation. The systematic review was performed in 2025 by searching for keywords like "pesticide biotransformation," "pesticide toxicity," and "pest management practices" in the PubMed, Scopus, and Web of Science scientific databases, without any time restrictions. The findings of this research indicate that the biotransformation of pesticides by microorganisms represents a pivotal process governing the fate of these chemicals in the environment, occurring mainly through three pathways: enzymatic degradation, co-metabolism, and complete mineralization. Plants generally have a much lower capacity to degrade pesticide residues than microorganisms; thus, their primary strategy is to detoxify and sequester pesticides within their cells instead of achieving full mineralization. The degradation of pesticides in the natural environment can also be accomplished through chemical degradation and photodegradation. Crucial chemical pathways involved in pesticide degradation include hydrolysis, along with oxidation and reduction reactions. In light of the escalating concerns regarding pesticide toxicity, it is important to implement sustainable management practices in the agricultural sector that focus on reducing pesticide toxicity in the soil. The first step in reducing the toxicity of pesticides in soils is to decrease their use by maximizing treatment effectiveness, minimizing the number of interventions, and lowering application rates. Applying agricultural practices like crop rotation, intercropping, organic farming, habitat management, and regular monitoring of pest populations substantially contributes to reducing pesticide toxicity in the soil. These practices not only mitigate pesticide-related soil contamination but also improve sustainable agricultural output and ecosystem resilience.