Purpose Role of omega-3 fatty acid (omega-3 FA) in human health and negative impact of altered omega-6 to 3 ratio is well documented. Hence, food fortification with omega-3 FA is need of the day. Functional foods containing omega-3 FA are gaining a lot of importance. However, long-term stability of omega-3 FA is a major obstacle with respect to the consumer acceptability and industrial exploitation of such functional food. The present study was a systematic attempt to assess the stability and acceptability of omega-3 FA emulsified formulation. Method Formulation was developed using flax oil with micronutrients and antioxidants at different doses (2-5 g/serve). The formulations were evaluated for long-term storage stability using various parameters such as oxidative stability, fatty acid analysis, optical microscopy, particle size analysis and zeta potential evaluation, colour analysis, and cryo-scanning electron microscopic analysis. Finally, the formulation was subjected for sensory evaluation using a 9-point hedonic scale to understand the overall acceptability of the formulation. Results There were significant alterations in oxidative stability parameters (p < 0.001), colour (p < 0.001), and zeta potential (p < 0.05), and marginal alterations were noted in fatty acid profile at the end of the 12 months. Microscopic studies showed homogeneity, uniformity in the morphological characteristics of the formulation, confirming the stability of omega-3 FA in the formulation. Sensory evaluation by 9-point hedonic scale revealed overall acceptability of the formulation in both water and milk. Conclusion The formulation (5 g/serve) was found to be stable up to 12 months, and consumer acceptability using sensory evaluation was proved.