The present study was undertaken to find the most suitable organic substrates for the biomass production, viability and efficacy of the biocontrol strain Trichoderma harzianum AS12-2 in the solid-state fermentation system. In total, 13 inexpensive, locally available substrates (agricultural wastes or by-products) were inoculated with the antagonist, and following one month of incubation at room temperature, all colonized substrates were air dried and ground to powder. The shelf life and viability of the Trichoderma strain were assessed as colony-forming units per gram (CFUs g−1) of each substrate on a monthly basis for up to one year at room temperature (25 ± 2 °C) and in the refrigerator (4 °C). In order to find out the effect of the substrate on the bioefficacy of T. harzianum AS12-2, the biocontrol potential of the formulations was evaluated against rice sheath blight disease caused by Rhizoctonia solani. The results showed that the fungus colonized more or less all substrates after one month, although the degree of colonization and conidiation was different among the substrates, being especially high in broom sorghum grain, rice husk, rice straw, rice bran and sugar beet pulp. Analysis of variance (ANOVA) of the population in the substrates in “Month 0” showed that the effect of treatment was significant, and the means were significantly different. The maximum population was recorded for broom sorghum grain and rice straw (6.4 × 1010 and 5.3 × 1010 CFUs g−1, respectively). The population declined in all substrates after one year of incubation at room temperature. This decline was relatively smaller in broom sorghum grain, rice straw and rice husk. On the other hand, the population in the same substrate incubated in the refrigerator was decreased in a mild slope, and the final population was high. In addition, the results of greenhouse assay showed that all bioformulations were effective in controlling the disease, and there were no significant differences among the substrates. According to the results of this study, broom sorghum grain, rice husk, rice straw, sugar beet pulp and cow dung could be recommended as suitable fermentation media for the industrial-scale production of T. harzianum strains.