The goal of the present study was to characterize anatomical and biochemical changes in rice plant roots in response to seed treatment with rhizobacteria (Burkholderia pyrrocinia (R-46) + Pseudomonas fluorescens (R-55)) and Trichoderma asperellum (Ta: mixture of strains T-06, T-09, T-12, and T-52). The experimental design was completely randomized, with six treatments (R-46, R-55, R-46 + R-55, Ta+ R-46 + R-55, Ta, and control) and ten replicates. Treatments Ta and R-46 + R-55 increased the root length and diameter as well as the cortex expansion and induced a 2% expansion of the aerenchymal space. Treatments Ta and R-46 increased the vascular cylinder diameter. The number of protoxylem poles and metaxylem vessel elements was increased by R-46 and R-55. The total phenol content increased with treatments Ta, R-46 + R-55, R-46, and R-55, and all the treatments increased the flavonoid content. The lignin content increased with the Ta and R-55 treatments. All the root architecture modifications resulting from the interaction between seedlings and bioagents (rhizobacteria and Trichoderma spp.) observed in the present study favored the root plasticity of rice seedlings.