Nutrition-Sensitive Agriculture (NSA) is a novel concept in agriculture that considers not only yield, but also nutritional value of produce, sustainability of production, and ecological impact of agriculture. In accordance with its goals, NSA would benefit from applying microbial-based products as they are deemed more sustainable than their synthetic counterparts. This study characterized 3 plant-beneficial bacterial strains (Paenibacillus pasadenensis strain R16, Pseudomonas syringae strain 260-02, Bacillus amyloliquefaciens strain CC2) on their biocontrol activity and effect on nutritional and texture quality of romaine lettuce plants (Lactuca sativa) in greenhouse. The pathogens used in the trials are Rhizoctonia solani and Pythium ultimum. The obtained results indicate that strain R16 had a significant ability to cause a statistically significant reduction in the symptoms caused by both P. ultimum (reduction of 32%) and R. solani (reduction of 42%), while the other two strains showed a less efficient biocontrol ability. Indices of the nutritional quality (content in phenols, carotenoids and chlorophyll) were unaffected by the treatments, indicating that the product was equivalent to that obtained without using the bacteria, while the texture of the leaves benefits from the biocontrol treatments. In particular, the mechanical resistance of the leaves was significantly higher in non-treated plants affected by R. solani but was restored to the values of healthy plants when the bacterial inoculants were present as well. The ecological impact was evaluated by characterizing the bacterial microbiota in bulk soil, rhizosphere, and root in the presence or absence of the inoculants. The composition of the microbiota, analyzed with a Unifrac model to describe beta-diversity, was radically different in the rhizosphere and the root endosphere among treatments, while the bulk soil formed a single cluster regardless of treatment, indicating that the use of these treatments did not have an ecological impact outside of the plant.