The aim of this study was to investigate how diets containing partially deshelled or whole krill meals affected growth, digestibility of main nutrients, faecal excretion of minerals, fluoride accumulation, and organ indices and health parameters in Atlantic salmon ( Salmo salar). Three extruded diets were fed for 100 days to salmon with an average weight of 550 g, distributed into 9 tanks equipped with flow through sea water. The dietary treatments comprised a control diet based on high-quality fish meal (FM) and two experimental diets where the FM was substituted with either partially deshelled krill meal (PDKM) or whole krill meal (WKM). Shell removal reduced the chitin content from 28 to 8 g kg −1 dry matter (DM), while fluoride was only reduced from 940 to 631 mg kg −1 DM. Growth rate for fish fed WKM was significantly lower than for salmon fed control diet whereas the PDKM diet did not appear to alter growth during the first feeding period. Digestibility of lipid tended to be higher for PDKM and lower for WKM compared to the FM control. No significant difference was seen for digestibility of nitrogen, but fish fed the FM diet had higher digestibility of threonine, serine, glutamine, histidine and lysine compared to fish fed the WKM diet. No major differences in plasma were seen for triacylglycerols, free fatty acids, glucose, total protein, albumin, globulin, urea, and total bilirubin. Trypsin activities in the pyloric and mid intestine were lower in fish fed the WKM diet compared to FM. Bile acid concentration in the pyloric intestine were significantly lower in fish fed the WKM diet compared to FM and PDKM. Fish fed both diets containing krill meal had signs of mild to moderate nephrosis. To conclude, PDKM could successfully replace FM as a sole protein source for Atlantic salmon, whereas the WKM slightly reduced growth rate compared to the FM and the PDKM diet.