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Wood pellets can sustain the growth of <i>Trichoderma</i> spp. in soil; however, little is known about their side effects on the microbiota. The aims of this study were to evaluate the effect of wood pellets on the growth of <i>Trichoderma</i> spp. in bulk soil and on the soil microbial population’s composition and diversity. <i>Trichoderma atroviride</i> SC1 coated wood pellets and non-coated pellets were applied at the level of 10 g∙kg⁻¹ of soil and at the final concentration of 5 × 10³ conidia∙g⁻¹ of soil and compared to a conidial suspension applied at the same concentration without the wood carrier. Untreated bulk soil served as a control. The non-coated wood pellets increased the total <i>Trichoderma</i> spp. population throughout the experiment (estimated as colony-forming unit g⁻¹ of soil), while wood pellets coated with <i>T.</i> <i>atroviride</i> SC1 did not. The wood carrier increased the richness, and temporarily decreased the diversity, of the bacterial population, with <i>Massilia</i> being the most abundant bacterial genus, while it decreased both the richness and diversity of the fungal community. Wood pellets selectively increased fungal species having biocontrol potential, such as <i>Mortierella</i>, <i>Cladorrhinum,</i> and <i>Stachybotrys</i>, which confirms the suitability of such carriers of <i>Trichoderma</i> spp. for soil application.