Tremendous increase in anthropogenic activities and natural disasters have created long term negative impacts to the crop productivity as well as on our ecosystem. In the debate regarding the ongoing ecosystem fluctuations, there is a need to explore an efficient, cost-effective, target-oriented and less manpower-based technologies for sustainable development. Microbial engineering provides a better solution for the growth of a healthy environment and higher agricultural productivity over the existing methods and resolved the challenges worldwide related to development of sustainable agriculture and greener ecosystems. In recent years, researchers are working on the development of different advanced microbial engineering strategies such as gene editing, CRISPR/Cas9, and RNAi to enhance the potential of microorganisms towards higher plant productivity and degradation of pollutants. The present review focused on the potential applications of genetically engineered microbial inoculants for sustainable agriculture and greener ecosystem development.