• Omics-based analysis reveals distinct metabolic potentials of eight biocontrol fungi, linking extracellular degradation and secondary metabolism to biocontrol efficacy.
• Paecilomyces lilacinus exhibits predatory biocontrol via abundant hydrolases that degrade pathogen protective barriers, enabling direct field application.
• Trichoderma species function as antibiosis-active agents, producing diverse secondary metabolites and forming dominant strains on preferred substrates.
• Understanding the metabolic transformation between primary and secondary metabolism provides a theoretical basis for optimizing large-scale biocontrol strategies.