This study aimed to produce an economic and stable biofungicide based on a new effective antagonistic strain (Trichoderma harzianum JF419706) via the exploitation of agro-industrial lignocellulosic residues as carriers for fungal growth to control the root rot diseases of vegetable crops. Trichoderma harzianum JF419706 showed a good resistance to a chemical fungicide with two-fold of the recommended dose. It was able to propagate on corn stovers amended with 20% of date molasses, as a very cheap substrate, up to 2.90 × 1016 CFU/g after 30 days. Formulation of the bioagent on the substrate as a fine powder (FTB) increased the shelf-life up to 8 months with good viability (9.37 × 1011 CFU/g). The bioagent propagated itself in the rhizospheric soil about two-fold of the initial inoculum. Application of the FTB, as a seed treatment, suppressed the root rot disease severity percentage of cucumber, lettuce, and tomato plants to 70.0%, 61.5%, and 53.8%, respectively, from the control. The crop yield increased by 50%, 35%, and 30% in the same order of the three crops. FTB promoted the growth and physiological processes of the plants significantly compared with the control. Our study recommends the application of the FTB as a cost-effective biofungicide and biofertilizer in crop management, singly or as a part of integrated pest management, to ensure the sustainability of green farming and reduce the chemical input in cultural practices.