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Triplicate groups of triploid and diploid Atlantic salmon were fed diets with a low (LP, total P: 7.1 g kg−1), medium (MP, total P: 9.4 g kg−1) or high (HP, total P: 16.3 g kg−1) phosphorous (P) level from first feeding (0.18 g) to transfer to sea water (~50 g, duration: 203 days) and subsequently fed a commercial diet in sea water for 426 days (~3 kg). This study examined the short- and long-term effects of dietary P on freshwater performance (mortality, growth), vertebral deformities (radiology), bone cell activity (ALP and TRACP enzyme activity in vertebrae and scales, and fgf23, bgp and igf-I relative gene expression in vertebrae), bone mineralization (ash content) and some parameters related to fish condition (heart and liver size). Irrespective of ploidy, at seawater transfer, fish fed the MP diet had significantly highest length and weight and those fed the LP diet significantly lowest length and weight, while those fed the HP diet had intermediate lengths and weights. Increased dietary phosphorus reduced deformities in both ploidies at seawater transfer; however, triploids fed the LP and MP diets had more deformities than diploids fed the respective diets, while there was no ploidy effect observed for fish fed the HP diet. The vertebral bone ash content at seawater transfer was significantly higher in diploids than in triploids when fed the MP diet only. Alkaline phosphatase (ALP) and tartrate-resistant acid phosphatase (TRACP) enzyme activities and relative gene expression of bone hormones involved in metabolism of plasma phosphate (fgf23) and bone growth (bgp) were not affected by ploidy at seawater transfer, but by dietary P level; LP increased ALP activity and reduced TRACP activity and fgf23 and bgp expression levels in vertebral bone. In scales, LP increased both ALP and TRACP activity. At the termination of the seawater period, the group-wise pattern in occurrence of vertebral deformities was the same as at seawater transfer. The present results on mortality, growth, bone mineralization and development of skeletal deformities all demonstrate that triploids have a higher P requirement than diploids in fresh water. This study shows that an optimalization of P nutrition for triploid Atlantic salmon can improve health and welfare and reduce down-grading of triploid salmon.