Dietary intake of n-3 long chain (LC) polyunsaturated fatty acids (PUFA) are recommended for their beneficial effects on human health, especially to prevent the development of metabolic diseases. However, the bioavailability of these PUFAs and their metabolic impact could be modulated by their chemical carriers (triacylglycerols, TG or phospholipids, PL). In addition, these PUFA are susceptible to lipid peroxidation. If they are not protected from oxidation, they can form toxic reactive species such as 4-hydroxy-hexenal (4-HHE). In this context, the aim of our study was to evaluate the impact of enriching high-fat diets with n-3 PUFA (i) bound to TG or PL and (ii) in unoxidized or oxidized form on the generation of inflammation and oxidative stress, and to understand some underlying mechanisms associated with intestinal absorption and reactivity of 4-HHE. On the one hand, our study confirmed in mice that the consumption of n-3 PUFA protects against oxidative stress and inflammation induced by high-fat diets. However, compared to TG, n-3 PUFA in the form of PL reduce the size of adipocytes and stimulate the antioxidant system. On the other hand, our study showed that the consumption of moderately oxidized n-3 PUFA results in increased plasma concentrations of 4-HHE and of inflammatory markers. In addition, activation of inflammatory pathways as well as endoplasmic reticulum stress were detected in the small intestine. Our results in vivo and in vitro, using intestinal Caco-2/TC7 cells, indicate that this can be partly due to the intestinal absorption of the end-product of n-3 PUFA oxidation, 4-HHE. In the context of the development of foods containing LC n-3 PUFA, our results contribute to identify the most effective PUFA carriers on a metabolic standpoint. Regarding public health and clinical practice, our results provide new basis for the set up of best practices regarding production and storage of food and supplements enriched with LC n-3 PUFA to avoid their lipid oxidation and its possible deleterious effects.