Fusarium head blight (FHB) is an economically important disease of small grains globally and is primarily caused by Fusarium graminearum in North America. Recently, microbial biocontrols have risen in importance as sustainable agents of disease control. However, the path to implementation of microbial biocontrols in agriculture will require an understanding of how microbiota impact both plant performance overall and vary with inherent host disease resistance. Using a full-factorial, controlled greenhouse experiment, we tested how bacterial endophyte treatments impacted both plant physiology prior to disease onset and FHB disease progression in Triticum aestivum (wheat). Seven bacterial endophytes were tested as seed soaks on two wheat varieties varying in FHB resistance. Leaf-level physiology and morphology measurements were made prior to inoculation with F. graminearum, while F. graminearum toxin accumulation (deoxynivalenol or DON) was quantified post-harvest. Bacterial endophyte treatments strongly impacted the light dependent reactions of photosynthesis, with changes in plant traits regulating light energy allocation and the build-up of electrochemical energy storage across the thylakoid membrane. Physiological responses were contingent on host variety. The direct effects of bacterial endophytes on wheat response to infection were weak and dependent on the inherent disease resistance of the host variety. However, disease outcomes were indirectly mediated by bacterial impacts on plant traits, with proton motive force traits emerging as common predictors of disease response across both host varieties and other traits indicating potential trade-offs in host response to bacterial inoculants and F. graminearum infection. Our results provide an alternate mechanism for microbial biocontrol efficacy other than direct antagonism with the pathogen inside the host. Furthermore, the chlorophyll-fluorescence and absorbance-based markers assessed here may have translational potential as a phenotyping tool for FHB susceptibility in wheat and other small grains.