Aquaponic system in greenhouses which can recycle and reuse the water and nutrients is gaining importance across the world to counter the uncertainties due to weather fluctuations. However, there is a slow pace of growth in aquaculture practices around the globe in general and India in particular. There are many barriers to adopt the aquaponic culture. In this study an analysis of the barriers for aquaponics culture in Indian context during the COVID-19 period is presented. Literature review and interactions with various stakeholders help to find out the list of potential factors while gauging the success of their prospective aquaponics project. The “best-worst” methodology (BWM) is employed for ranking of barriers, whereas categorizing of barriers is carried out with the help of fuzzy DEMATEL. Furthermore, the results of this research work are of great value to corporations or start-up companies looking to invest in this technology as well as to farmers who wish to adopt this farming technique.