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Agro-industrial residues represent more than 60% of organic wastes worldwide, which could be used to generate other by-products or to be incorporated into other production chains. For example, bagasse is a waste from the tequila industry in Mexico that could be implemented for mushroom cultivation. Additionally, the substrate influences the growth, development, and production of secondary metabolites of fungi. This work presents a comparative experiment that studies the metabolite production in Pleurotus djamor mushrooms on agave bagasse and barley straw (traditional substrate). The biological efficiency (BE), yield, phenolics and flavonoids, antioxidant capacity, tannins, and the identification of low molecular weight metabolites were evaluated. Five treatments were proposed according to the following mixtures of agave bagasse: barley straw: T1 (1:0), T2 (3:1), T3 (1:1), T4 (1:3), and T5 (0:1). T2 had the highest yield (13.39 ± 3.23%), BE (56.7 ± 13.71%), and flavonoids (44.25 mg rutin equivalent (RE)/g); T3 obtained the highest phenol content (230.27 mg GAE/g); and T1 the highest tannins content (0.23 mg (+) catechin equivalent (CE)/g). Finally, T1 and T5 are the ones that present the greatest number of primary metabolites, including hydroxycitric acid, 2-deoxy-D-galactose, D-mannose, paromomycin, palmitic acid, pyrrole, mannitol, and DL arabinose, while in T2, T3, and T4 only two chemical compounds were found present (palmitic acid and pyrrole in T2, silicic acid and pyrrole in T3 and 2-deoxy-D-galactose and quinoline in T4). The cultivation substrate influences the concentration of bioactive molecules in the fruiting bodies of P. djamor. Additionally, P. djamor’s degradation of agave bagasse residue generates a potential application for agro-industrial residue management at a low cost.