There is currently renewed interest in farming triploid Atlantic salmon. Improving farming requires identifying triploid specific phenotypic and physiological traits that are uniquely derived from ploidy per se and developed under optimal growing conditions. This study investigated firstly, the impact of ploidy on growth performance and whole body composition of Atlantic salmon at different early freshwater stages [34dph (days post-hatching) alevin, 109dph fry, and 162dph parr] and secondly, whether phenotypic differences at these stages were reflected in protein samples collected from whole fish, white muscle or liver tissue. Female diploid and triploid Atlantic salmon (n=3) were first fed at 35dph and then maintained by feeding to satiation on commercial feeds. Triploids were significantly lower in weight at the late alevin and fry stages but matched diploid weight at the parr stage. The whole-body lipid content was significantly higher for triploids at the parr stage, while the whole-body lipid class profile was broadly similar and was largely not affected by ploidy. Comparative label-free shotgun proteomic analysis did not detect significant alterations in protein expression between diploids and triploids at any growth stage. The present results indicate that ploidy under optimal growing conditions and during early freshwater stages only result in small phenotypic differences in weight and whole body lipid content that were not reflected at the proteome level. These findings suggest that optimal husbandry conditions for freshwater Atlantic salmon are similar between ploidies, at least for all-female populations.