This study conducted a thorough investigation into the impact of two emulsification techniques, namely high-pressure homogenization (HPH) and microfluidization (MF), on the emulsification of krill oil. The comprehensive analysis encompassed various aspects, including particle size characterization, structural assessment, oxidative stability evaluation during storage, measurement of bioaccessibility, and in vitro simulated digestion analysis. Emulsions produced through MF exhibited several noteworthy advantages over those generated by HPH. Most prominently, MF-prepared emulsions featured smaller and more uniformly distributed particles, in stark contrast to the less uniform particles generated by HPH. Moreover, MF-based emulsions demonstrated significantly enhanced oxidative stability during storage, with astaxanthin degradation occurring at a substantially lower rate (38.11% for HPH compared to 89.44% for MF). When assessing emulsion behavior during in vitro simulated digestion, microfluidization formulations exhibited superior stability and markedly higher bioaccessibility in comparison to their HPH counterparts. Of particular significance was the remarkable increase in the release of free fatty acids observed during the intestinal phase of digestion in MF emulsions, indicating an improved lipid digestion process. This study firmly establishes microfluidization as the superior method for crafting emulsions of krill oil, especially within the context of the food industry. Microfluidization not only ensures the preservation of oil quality during storage but also significantly enhances emulsion stability and promotes improved digestibility. These findings hold substantial promise for the development of delivery systems for n-3 fatty acids, making them suitable for incorporation into a wide range of commercial food, beverage, and pharmaceutical products.