The urgent need for sustainable alternatives to synthetic herbicides has intensified interest in biocontrol strategies, particularly those based on fungal secondary metabolites. This review provides a comprehensive overview of the diversity, biological activity, and potential applications of phytotoxic fungal metabolites in weed management. A total of 183 compounds are examined, grouped into five major chemical classes: 61 polyketides, 53 terpenoids, 36 nitrogenous metabolites, 18 phenols and phenolic acids, and 15 miscellaneous molecules. These metabolites are primarily produced by various fungal genera, which are well known for their capacity to generate bioactive compounds with strong phytotoxic properties.

The effects of these metabolites—often described through visible plant symptoms rather than detailed mechanistic insights—range from inhibition of seed germination and suppression of root and shoot elongation to severe tissue necrosis and organ malformation. Unlocking their potential requires advanced methodologies, including fungal cultivation under optimized conditions, metabolite extraction, phytotoxicity assays on model and target species, purification and fractionation of complex mixtures, and chemical identification using modern spectroscopic and chromatographic techniques.

Although most studies to date have been conducted under controlled laboratory conditions, translation to practical weed management demands rigorous evaluation in greenhouse and field environments. Such trials are essential to confirm efficacy against specific weed populations, assess selectivity toward non-target plants, and evaluate ecological safety. Furthermore, the integration of emerging technologies—such as nanomaterials for improved delivery, encapsulation, and stability—offers promising avenues for enhancing the performance and environmental compatibility of fungal metabolite-based bioherbicides.