Abstract Clostridium autoethanogenum protein (CAP) is an emerging protein source with several key advantages and it has investigated on juvenile turbot (9.13 g). However, it was indicated that fish growth stage is a decisive factor for CAP performance and the influence of CAP on turbot intestine health has not been reported. Thus, it is worth investigating the effects of CAP on turbot extensively. In the present study, a 67-day feeding experiment was conducted to evaluate the effects of CAP on turbot in the grow-out phase from growth performance, intestine and liver health. Six hundred and thirty turbot with an initial body weight of about 150 g were randomly divided into 6 groups, which were fed with fishmeal-based control diet or diet with CAP to replace 15%, 30%, 45%, 60% and 75% of fishmeal protein in control diet, respectively. From growth and feed utilization, the substitution level of CAP should no more than 30%, which was less than previous reported on juvenile turbot. The palatability of the feed was linearly reduced. Although CAP did not induce enteritis, it decreased the intestine villi height in middle and intestine villi density in distal intestine. Except for decreasing the size of hepatocytes by CAP at 45% or higher substitution levels, no other abnormality observed in liver histology. However, dietary CAP reduced the triglyceride and cholesterol levels in the plasma at 30% or higher levels and linearly down-regulated genes related to lipogenesis in liver. The genes related lipid transportation and oxidation were up-regulated by CAP at the substitution levels of 15–60%. The present work confirmed the safety of CAP in fish feed and suggested more work should be conducted before it widely used in aquafeed.