The present study was carried out to compare S. indica, and more specifically its encapsulated spores, with effective microorganisms (EM: a commercial biofertilizer) on the growth and yield of maize plants under drought stress. A completely randomized factorial design was done with five levels of inoculums (non-inoculated, encapsulated spore and mycelium of S. indica, EM fertilizer as well as combined Si mycelium/EM) and two levels of drought stress [Filed capacity (F.C.) and 50% F.C.]. The results showed that drought stress significantly decreases biomass, photosynthetic pigments, nutrient concentration, and yield concomitantly with increasing antioxidant activities, malondialdehyde, carbohydrates, and proline content. The results also revealed that plants treated with S. indica inoculums and EM fertilizer show enhancement in plant biomass and yield compared to untreated plants. An increase in photosynthetic pigments, carbohydrate, protein, proline, potassium, phosphorous, and antioxidant enzymes was also recorded with S. indica inoculums and EM fertilizer-treated plants over untreated plants under drought stress. Additionally, endophyte inoculums and EM fertilizer decreased malondialdehyde content. Interestingly, encapsulated spores had the same positive and comparable effect to mycelium and EM. Overall, different inoculums of S. indica and EM fertilizer, alone or in combination, can modulate the effect of drought stress and decrease its adverse effects by enhancing plant physiological responses. Hence, the findings demonstrate that the application of inoculums of S. indica including encapsulated spores is beneficial in coping with drought stress.