The growing demand for sustainable agricultural inputs has encouraged the development of biotechnological alternatives based on microbe-derived enzymes and bioactive metabolites. In this study, co-fermentation strategies involving different Trichoderma strains were investigated as a process-based approach to enhance the production of enzymes and plant growth-promoting metabolites with agricultural relevance. Distinct culture media compositions and inoculation strategies significantly affected microbial performance and biocatalytic outputs. Optimized co-culture conditions resulted in enhanced conidiation, microsclerotia formation, siderophore production (up to 95%), phosphate solubilization (up to 419 mg mL⁻¹), indole-3-acetic acid synthesis (0.60 mg mL⁻¹), and increased activities of chitinase, β-1,3-glucanase, and protease. Metabolomic profiling by GC-MS revealed the induction of diverse secondary metabolites associated with antimicrobial activity and plant–microbe signaling. Overall, the results demonstrate that Trichoderma co-fermentation is an effective biotechnological strategy to intensify enzyme and metabolite production, highlighting its potential for the development of multifunctional bioinputs for sustainable agricultural applications.