Plant-associated microbiome (phytobiome) is recognised to play an important role in plant development, improving plant resilience against abiotic and biotic stresses. Biocontrol of plant diseases is promoted as a key component of integrated pest and disease management for sustainable agriculture. Augmented introduction of biocontrol microbes is expected to affect the resident phytobiome, which could lead to unintended consequences. We conducted research studies to assess the effects of three microbes (Gliocladium catenulatum, Trichoderma asperellum and Bacillus subtilis) on communities of living microbes on strawberry grown in table-top coir bags under protection. G. catenulatum and T. asperellum were applied to strawberry roots via drenching soon after planting, and. G. catenulatum and B. subtilis were sprayed onto open flowers. To specifically profile communities of living microbes, we used to a PMAxx™-based method to treat samples before DNA extraction. Amplicon-sequencing was used to profile flower epiphytes whereas shot-gun sequencing was used for root epiphytes. Applying the three biocontrol microbes was successful, leading to significant increases in the relative abundance of the target microbes on both flowers and roots. The two introduced fungal taxa (G. catenulatum and T. asperellum) appeared to affect mainly fungal microbiome components whereas the introduced bacterial taxona (B. subtilis) mainly affected bacterial microbiome components. The effects of introduced biocontrol microbes on the resident microbiome was more profound and long-lasting on roots than on flowers. Although biocontrol organisms led to significant changes in the overall microbial composition, their effects on individual microbial taxa groups were limited. The present research suggests that biocontrol of root pathogens may hold a greater promise than flower/fruit diseases.