The present study was conducted to strengthen the knowledge on gut immune functions and health in Atlantic salmon under large scale, commercial conditions in the Arctic region of Norway. Two groups of fish were monitored, one fed a series of diets without functional ingredients (Ref) and the other diets with functional ingredients (Test). The nutritional composition of the two diet series varied in parallel according to the nutrient requirements of the fish during the observation time. The content of functional ingredients in the Test diets, i.e. nucleotides, yeast cell walls, a prebiotic and essential fatty acids, varied in accordance with a strategy developed by the feed company. The fish were observed at four sampling time points, the first (FW) in May 2016 two weeks before seawater transfer, the other three throughout the following seawater period until the fish reached a size of about 2 kg, i.e. in June, four weeks after seawater transfer (SW1); in November (SW2), and in April the following year (SW3). Gut health was assessed based on histopathological indicators of lipid malabsorption and gut inflammation, expression of gut immune, barrier and other health related genes, plasma biomarkers, somatic indices of intestinal sections, as well as biomarkers of digestive functions. Seawater transfer of the fish (SW1 compared to FW) caused a marked lowering of expression of genes related to immune and barrier functions in the distal intestine, i.e. cytokines (il1β, il10, tgfβ, ifnγ), T-cell markers (cd3γδ), myd88 and tight junction proteins (zo-1, claudin-15, claudin-25b), indicating suppressed immune and barrier functions. At SW2 and SW3, most of the immune biomarkers showed values similar to those observed at FW. The development of plasma cholesterol and triglyceride levels showed similar picture, with markedly lower levels after seawater transfer. Lipid malabsorption was observed in particular in fish from SW1 and SW2, as indicated by hyper-vacuolation of the pyloric caeca enterocytes with concurrently increased expression levels of plin2. Regarding effects of functional ingredients, significantly lower condition factor and plasma triglyceride level were observed for Test-fed fish at SW2, indicating a metabolic cost of use of a mixture of nucleotides, yeast cell walls and essential fatty acids. No clear effects of functional ingredients on expression of gut immune genes and other health indexes were observed through the observation period. The great, temporary lowering of expression of gut immune and barrier genes at SW1 is suggested to be an important factor underlying the increased vulnerability of the fish at this time point. Our findings regarding supplementation with functional ingredients raise questions whether some of these ingredients overall are beneficial or might come with a metabolic cost. Our results highlight the need for a better understanding of the cause and consequences of the suppression of gut immune functions of farmed Atlantic salmon just after seawater transfer, and the use of functional ingredients under commercial conditions.