Emerging economies, e.g. India, China and Brazil etc., face challenges to adopt food safety (FS) practices in their food supply chains. Considering food industry’s operations and processes, this study identifies 25 challenges to the FS initiatives involving the opinions of practitioners from six major Indian food producers and academic experts. The challenges are grouped into five categories, viz. organisational, government and policy, global, knowledge and financial. We identify the best and worst challenges to the FS initiatives along with causality among them using combined Best Worst Method (BWM) and ‘Decision Making Trial and Evaluation Laboratory’ (DEMATEL) approaches. BWM prioritises these challenges, while DEMATEL identifies causal relationship maps for the prioritised challenges. The BWM results demonstrate that the government and policy related challenges are the key challenges followed by the organisational, global, knowledge and financial related challenges. The DEMATEL results exhibit the organisational, government and policy, and global related challenges as the cause group challenges. The knowledge and financial related challenges represent the effect group challenges. Mitigation of these challenges inherently necessitates stakeholders’ involvement in the food supply chains. We identify constructs for food safety initiatives policy in the emerging economies to raise public awareness while encouraging greater collaboration and efficiency in food supply chains to help achieve the second Sustainable Development Goal (SDG) for securing food for everyone. The results of the study offer guidance and deeper insights to supply chain managers about synergy requirements between the government policymakers and key players of the industry in the emerging economies.