The liver health of Gilthead sea bream and European sea bass, fed with fish meal-free diets, including various proportions of plant proteins, as well as insect and poultry by-product meals, was investigated through biochemical and histological analyses using a new liver index (LI) formula. Four isoproteic (45% Dry Matter, DM) and isolipidic (20% DM) diets were compared, including a plant-based control diet (CV) and three other test diets, in which 40% of a plant protein-rich ingredient mixture was replaced with meals from Hermetia illucens (H40) or poultry by-product (P40) alone, or in combination (H10P30). The trials lasted 12 and 18 weeks for sea bream and sea bass, respectively. The results obtained thus far highlighted species-specific differences in the physiological response to dietary changes. In sea bream, the biochemical and histological responses suggest favorable physiological and liver health statuses, with higher serum cholesterol (CHO) and triglyceride (TAG) levels, as well as moderate hepatocyte lipid accumulation, with the H10P30 diet compared to the CV (p < 0.05). In sea bass, all diets resulted in elevated serum TAG levels and lipid accumulation in the liver, particularly in fish fed the P40 one (p < 0.05), which resulted in the highest LI, coupled with a higher frequency of severe lipid accumulation, hypertrophy, cord loss, peripheral nuclei displacement, and pyknosis. In conclusion, sea bream adapted well to the test diets, whereas sea bass exhibited altered hepatic lipid metabolism leading to incipient liver steatosis, likely due to the high lipid contents of the diets, including the insect and poultry meals. The LI formula developed in this study proved to be a reliable tool for assessing the effects of dietary changes on the liver health of sea bream and sea bass, consistent with biochemical and histological findings.