Three groups of European sea bass (Dicentrarchus labrax) were fed for seven months, with either a conventional diet or two different organic diets, which contain organic vegetables and a natural antioxidant compound. The two organic diets differed themselves in terms of raw proteins, fish oil, and lipid contents. Sea bass welfare condition was assessed in relation to these three diets, using 16 different indicators. These were: swimming activity (recovery test, muscle activity), haematological and serological stress indicators (haematocrit, haemoglobin, red-blood-cell count, cortisol, glucose, lactate), aspecific immunity parameter (lysozyme), indicators of exposure to organic contaminants (7-ethoxyresorufin-O-deethylase and glutathione-S-transferase), and growth parameters (weight gain, specific growth rate, feed conversion ratio, protein efficiency ratio, and hepato-somatic index). Most of these parameters individually did not give consistent responses, but their integration can provide an accurate evaluation of the fish welfare conditions among the three diet experimental groups. The multiparametric approach outlined a comprehensive picture of sea bass physiological state. The principal component analysis and the multi-criteria-decision-analysis were found to be useful tools for an integrated fish welfare assessment, highlighting that the best welfare condition was achieved in the experimental group fed with the protein-rich organic diet.