This study was the first to investigate the effect of soy antinutrients, saponins and phytosterols, in on-growing sea bass. Seven diets were formulated: a control diet (fishmeal and fish oil based) and six diets containing 1 or 2 g kg−1 levels of soya saponins, 5 or 10 g kg−1 levels of phytosterols or a combination of 1 g kg−1 saponins + 5 g kg−1 phytosterols or 2 g kg−1 saponins + 10 g kg−1 phytosterols. After a 59 days feeding trial fish were weighed, faeces collected for digestibility studies and plasma sampled for cholesterol quantification. At day 15 and 59, distal intestine (DI) samples were collected for histological evaluation and quantification of maltase (Malt), alkaline phosphatase (AlP) and leucine aminopeptidase (LAP) activities. At day 59, DI was collected for gene expression of AlP, Malt and immune related genes. Antinutrients had no effect on fish performance, digestibility, plasma cholesterol levels and digestive enzymes activities and gene expression. Only mild morphological changes were present in groups fed high levels of saponins + phytosterols. Expression of immune related genes showed no differences between groups. Overall, on-growing sea bass showed high tolerance to dietary antinutrients up to the levels tested.