The natural structure of whole food plays an important role in the physiological impact of bioactive compounds present within the food, also known as the "matrix effect". Long-chain omega-3 polyunsaturated fatty acids (LCn-3PUFAs) are one example of a food-derived nutrient, mostly found in fish, that is believed to be influenced by the food matrix. However, most previous studies have compared only the long-term bioavailability of fish versus fish oil and have used commercial sources of fish oil. The present study aimed to investigate whether fish (salmon) matrix influences the transit of LCn-3PUFAs during in vitro digestion and affects bioavailability in healthy females. Meals containing intact salmon (intact structure), minced salmon (some structure) and defatted salmon + oil (no structure) with identical macronutrient compositions were developed. Healthy female participants (n = 13) consumed the meals in a postprandial crossover study and blood was collected at regular time points for 6 h post meal consumption. In parallel, in vitro digestion of the meals was performed using a human gastric simulator (HGS) and digesta samples were collected at regular time points for 6 h. Results: showed that plasma concentration of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) were significantly higher after participants consumed intact salmon compared to the other meals (covariate analysis p < 0.001). The in vitro digestion results showed defatted salmon + oil meal had a faster decrease in pH and faster fat emptying from the HGS than the other two meals. The defatted salmon + oil meal more closely followed fat emptying of a homogeneous unstructured meal, whereas the other meals exhibited phase separation with a delay in fat emptying. Conclusion: The fish matrix (salmon) plays an important role in the bioaccessibility and bioavailability of EPA and DHA. The differences are partly explained by fat digestion and emptying from the stomach. This study suggests that the natural structure of fish has a functional effect on the absorption and bioavailability of fish oil.