This study aimed to elucidate the effects of two soy antinutrients, saponins and phytosterols, on growth, intestinal health and function of European sea bass juveniles. Seven fishmeal-based diets were formulated: a control diet without antinutrients and six experimental diets containing low or high levels of soyasaponins (SapL and SapH, respectively), low or high levels of phytosterols (PhytL and PhytH, respectively) and low or high levels of soyasaponins + phytosterols (SapPhytL and SapPhytH, respectively). A feeding trial was conducted for 59 days after which blood was collected for plasmatic cholesterol quantification and intestinal samples were collected for histology, digestive enzymes activity and gene expression analysis. Histology was also performed at day 15. PhytL resulted in high distal intestine (DI) relative weight and decreased plasma cholesterol, while PhytH caused inflammatory changes in the DI. SapH depressed maltase and alkaline phosphatase activity in DI and the histological evaluation indicated some inflammatory changes. The SapPhytH resulted in decreased maltase activity in the DI and indications of inflammatory changes that were supported by the results on gene expression profiles. The antinutrients tested did not compromise growth, however, caused some gastrointestinal disturbance that may affect fish in the long term.