The effects of replacing dietary fish meal (FM) and oil (FO) with plant ingredients on absorption, metabolism, and flesh retention of astaxanthin were tested in Atlantic salmon. Phospholipid (PL) concentrates of marine (MPL) or plant origin (Soy lecithin, SoyLec) were supplemented to plant-based diets as choline sources to study potential effects on astaxanthin absorption and retention. A total of six diets were tested, three of them at high and low temperature (6 and 12°C). Lower temperature and slower growth increased retention of astaxanthin in the muscle of the marine-diet group but had no effect in the low marine-diet groups. Digestibility of astaxanthin was not affected by temperature in any of the diet groups. Sufficient PL in the diet was crucial for the digestibility of astaxanthin and lipids, but the source of phospholipid did not affect digestibility. The source of PL did have an effect on the accumulation of astaxanthin in the muscle. MPL reduced the muscle retention of astaxanthin and increased liver accumulation of the astaxanthin metabolite idoxanthin compared to plant protein (PP) diets and diets supplemented with SoyLec. PP diets also increased the deposition of lipid in liver and caused steatosis of intestine. Genes involved in formation of lipoproteins and cholesterol synthesis in the mid-intestine were downregulated in fish fed PP diets compared to a FM diet. MPL supplementation to the PP diet reduced the changes in gene expression and the steatosis in the intestine whereas adding SoyLec did not. Neither MPL nor SoyLec supplementation reduced the accumulation of lipid in liver in fish fed plant protein diets. In conclusion, the addition of MPL to a plant-based diet improved intestinal lipid transport, but not astaxanthin deposition in muscle.