The strains of Trichoderma used as biocontrol agents show different mechanisms of action in their antagonistic interactions with fungal pathogens through direct and indirect effects. Direct effects include nutrient and space competition, volatile and non-volatile antibiotic production, hydrolytic enzyme production and parasitism. Indirect effects include all aspects that promote morphological and biochemical changes in the host plant, such as nutrient availability, stress response induction of resistance to diseases caused by plant pathogens. The secondary metabolites (SMs) are small molecules that are not directly essential for growth yet have important roles in signaling, development and interaction with other organisms. The production of Trichoderma secondary metabolites is strain dependent and varies in relation to the equilibrium between elicited biosynthesis and biotransformation rates.