Conventional chemical-based control methods for soil-borne diseases often degrade soil quality. The recycling of organic wastes offers a promising solution to simultaneously alleviate environmental pollution and restore soil health. As a beneficial fungus, Trichoderma plays a crucial role in enhancing plant performance. However, knowledge of the mechanisms through which organic wastes and Trichoderma interact to influence plant performance remains limited. We investigated how the combined application of organic wastes (chitin and straw) and a biocontrol fungus (Trichoderma) influenced the rhizosphere microbiome to improve plant performance. Compared with the control, organic waste alone, and Trichoderma alone treatments, the combined application of organic wastes and Trichoderma significantly (p < 0.05) increased cucumber yield and reduced pathogen density. Increased yield and reduced pathogen density were associated with changes in bacterial and fungal communities induced by this combined application treatment. Indeed, this combined application treatment enabled plants to recruit certain potentially beneficial core bacterial (e.g., Streptomyces and Flavisolibacter) and fungal taxa (e.g., Trichoderma), increasing their positive interactions in the rhizosphere. We demonstrate that the combined application of organic wastes and Trichoderma can shape distinct rhizosphere bacterial and fungal communities, promoting an increase in beneficial microorganisms and their positive interactions, which contribute to enhanced plant performance.