ABSTRACTManaging agrochemicals for crop production always remains a classic challenge for us to maintain the doctrine of sustainability. Intensively cultivated rice–wheat production system without using the organics (organic amendments, manures, biofertilizers) has a tremendous impact on soil characteristics (physical, chemical, and biological), environmental quality (water, air), input use efficiency, ecosystem biodiversity, and nutritional security. Consequently, crop productivity is found to be either decreasing or stagnating. Rice–wheat cropping system is the major agroecosystem in India feeding millions of people, which is widely practiced in the Indo-Gangetic Plains (IGP). Microorganisms as key players in the soil system can restore the degraded ecosystems using a variety of mechanisms. Here, we propose how delivery systems (i.e., the introduction of microbes in seed, soil, and crop through bio-priming and/or bioaugmentation) can help us in eradicating food scarcity and maintaining sustainability without compromising the ecosystem services. Both bio-priming and bioaugmentation are efficient techniques to utilize bio-agents judiciously for successful crop production by enhancing phytohormones, nutrition status, and stress tolerance levels in plants (including mitigating of abiotic stresses and biocontrol of pests/pathogens). However, there are some differences in application methods, and the latter one also includes the aspects of bioremediation or soil detoxification. Overall, we have highlighted different perspectives on applying biological solutions in the IGP to sustain the dominant (rice–wheat) cropping sequence.