The dependence on agrochemicals in modern agriculture has raised concerns about environmental impact and disruption of beneficial microbiomes. To address plant diseases with preserving ecological balance, there is a growing interest in eco-friendly alternatives including multiple species of Trichoderma, renowned biocontrol agents that enhance plant immunity and reduce disease incidence. This study explores the physiological changes in plants treated with Trichoderma and examines plant–fungal interactions to evaluate the efficacy of these biostimulants. The study focuses on the effects of both native (strain isolated from soil collected from farmers’ vegetable and cereal crop fields) and commercial Trichoderma spp. applications on the morpho-physiological responses and antioxidant enzyme activities of various crops, including okra, beans, millet, maize, and mustard. Results indicate variable impacts on antioxidant enzyme activities; notably, ascorbate peroxidase activity decreased in most treated plants except mustard, where it increased. Guaiacol peroxidase activity was generally reduced across all plant species treated with native Trichoderma strains. Furthermore, the plant growth parameters such as plant biomass and dry matter accumulation are positively correlated with SPAD chlorophyll index (soil plant analysis development), chlorophyll, PSII activity, and negatively correlated with antioxidant enzyme activity. By elucidating the physiological responses and interactions induced by Trichoderma treatment, the study underscores the importance of integrating such eco-friendly solutions into agricultural practices to promote both plant health and environmental stewardship. Particular attention can be given to elucidating the bidirectional molecular communication between Trichoderma and plant roots within the rhizosphere, as this interaction plays a critical role in modulating plant growth, enhancing stress tolerance, and activating defense responses through complex signalling pathways.