Remote sensing can offer stakeholders opportunities to make precise and accurate decisions on agricultural activities. For instance, farmers can exploit aircraft systems to acquire survey-level, high-resolution imagery data for crop and soil management. Therefore, the objective of this study was to analyze whether an unmanned aerial vehicle (UAV) allows for the assessment and monitoring of biofertilization of the common bean upon vegetation indices (VIs). The biological treatment of the legume crop included its inoculation with phosphate-solubilizing bacteria (PSB), namely Bacillus subtilis and B. megaterium. Indicators of photosynthetic performance, such as chlorophylls (a and b) and carotenoids, were measured from actively growing leaves to determine effectiveness. In addition, images were acquired in the field, both spatially and temporally, to establish functional relationships between biometric and computational features. Microorganisms manifested as growth-promoting agents to the crop as they significantly increased its quantities of light-harvesting pigments. VIs allowed for predicting their impact on photosynthetic performance, making them on-site markers of PSB. Therefore, this research can provide insights into the remote, non-destructive mapping of spectral changes in the common bean upon the application of PSB. Imagery data from UAV would enable producers to generate information on the crop to intervene in the field at the right time and place for improved utilization of biofertilizers.