Fungi of the genus Trichoderma produce secondary metabolites having several biological activities that affect plant metabolism. We examined the effect of three Trichoderma bioactive metabolites (BAMs), namely 6-pentyl-α-pyrone (6PP), harzianic acid (HA) and hydrophobin 1 (HYTLO1), on yield, fruit quality and protein representation of strawberry plants. In particular, 6PP and HA increased plant yield and number of fruits, when compared to control, while HYTLO1 promoted the growth of the roots, increased the total soluble solid up to 19% and the accumulation of ascorbic acid and cyanidin 3-O-glucoside in red ripened fruits. Strawberry proteomic analysis showed that BAMs influenced the representation of proteins associated with protein metabolism, response to stress/external stimuli, vesicle trafficking, carbon/energy and secondary metabolism. Results suggest that the application of Trichoderma BAMs affects strawberry plant productivity and fruit quality, and integrate previous observations on deregulated molecular processes in roots and leaves of Trichoderma-treated plants with original data on fruits.