Microbial inoculants for controlling soil pathogens are an environmentally sustainable approach for attaining agricultural intensification. Charcoal root rot pathogens might threaten global food security and degrade prime agricultural lands. Microbial antagonists to control charcoal root disease were not properly studied with reference to physiological and photochemical basis. This research was aimed to examine the impact of newly isolated microbial biocontrol agents (MBCAs) on growth and photosynthetic efficiency (photosystem II) in pathogen (Macrophomina phaseolina)‐infected plants. The MBCAs (Purpureocillium lilacinum and Aspergillus terreus) were isolated and seeds were coated to improve soil fertility and resilience of agricultural lands. Both MBCAs inhibited the colonization of pathogenic fungus around the roots of host plants. Decline in growth traits was observed due to the detrimental impacts of root rot disease on growth parameters compared with plants treated with M. phaseolina. However, the growth of corn plants in both soils with and without M. phaseolina infestations was substantially improved by treating corn seeds with P. lilacinum and A. terreus. The pathogen drastically reduced the distinct parameters of photosystem II of photosynthesis. However, applying P. lilacinum and A. terreus significantly improved the total performance index (PItot), size, and the number of active reaction centers of photosystem II (Fv/Fo), electron transport rate, electron trapping per absorption (TRO/ABS), electron transport per absorption (ETO/ABS), electron transport per trapping (ETO/TRO), and the efficiency of light reaction (φEo) but downregulates nonphotochemical quenching (NPQ). Our study demonstrates that microbial antagonists offer a more effective, ecofriendly alternative to improve the land to sustainable agriculture.