Pesticides, while essential for crop protection, act as chemical stressors that disrupt plant secondary metabolism─a critical mediator of environmental adaptation and crop quality. This review adopts a defense and detoxification mechanism-driven framework to analyze the mechanisms by which pesticides alter phytohormones, phenolics, volatile organic compounds, and specialized metabolites through direct phytochemical interactions, microbiome modulation, and soil environment shifts. We highlight pesticide-induced oxidative stress, transcriptional reprogramming, and enzymatic/nonenzymatic detoxification mechanisms, alongside effects via direct phytochemical interactions, microbiome modulation, and soil environment shifts. A comparative analysis of the differential impacts of distinct pesticide classes on plant secondary metabolism, with emphasis on molecular structural features and physicochemical properties. Integrating multiomics evidence, we elucidate the relationship between dynamic "pesticide-plant-microbe/soil" interactions and plant secondary metabolism. This review deepens the understanding of pesticide phytotoxicity from individual plants, plant-associated organisms, and soil environment, bridging molecular mechanisms with agricultural practices to balance crop protection and crop health.
Lin et al. (2025) studied this question.