Flaxseed has been recognized as a superfood worldwide due to its abundance of diverse functional phytochemicals and nutrients. Various studies have shown that flaxseed consumption is beneficial to human health, though methods of processing flaxseed may significantly affect the absorption and metabolism of its bioactive components. Hence, flaxseed was subjected to various processing methods including microwaving treatment, microwave-coupled dry milling, microwave-coupled wet milling, and high-pressure homogenization. In vitro digestion experiments were conducted to assess the impact of these processing techniques on the potential gastrointestinal fate of flaxseed oil. Even though more lipids were released by the flaxseed at the beginning of digestion after it was microwaved and dry-milled, the full digestion of flaxseed oil was still restricted in the intestine. In contrast, oil droplets were more evenly distributed in wet-milled flaxseed milk, and there was a greater release of fatty acids during simulated digestion (7.33 ± 0.21 μmol/mL). Interestingly, wet-milled flaxseed milk showed higher oxidative stability compared with flaxseed powder during digestion despite the larger specific surface area of its oil droplets. This study might provide insight into the choice of flaxseed processing technology for better nutrient delivery efficiency.