This study involved a rheological characterization of a W/O emulsion manufactured on a pilot scale using omega-3 fatty acids as part of the oil phase and butter milk as the emulsifier. Polyunsaturated omega-3 fatty acids are essential to prevent cardiovascular diseases, improve pulmonary function and also form part of the neurological structure. Buttermilk is a by-product of the dairy industry and has a high organic load which possesses surfactant properties and constitutes a good substitute for conventional emulsifiers in the food industry. The microstructural nature of the emulsion was characterized from the viscoelastic parameters and mechanical spectra. The linear viscoelastic range was determined, from which the maximum stress that the emulsion could withstand from the processing conditions without altering its microstructure was established. In addition, the storage stability of the emulsion was studied to instrumentally predict the rheological behaviour before sensory destabilization of the emulsion was observed. At the frequencies used, a significant decrease in dynamic viscoelastic parameters was periodically observed (G 'and G''), showing a structural change during storage. Furthermore, a coalescence phenomenon was observed after 18 months. The formulation with added omega-3 fatty acids and buttermilk provided a basis for obtaining a functional food as well as adding value to an industrial by-product.