This study investigated the effect of dietary Clostridium autoethanogenum protein (Ca P) on growth, whole-body composition, plasma parameters, and hepatic genes expression related to growth and AMPK/TOR/PI3K signaling pathway of the genetically improved farmed tilapia (GIFT: Oreochromis niloticus ) juveniles. The fish (initial weight of 0.7 ± 0.05 g) were fed with diets containing Ca P at 0 g/kg (Control, diet 1), 50 g/kg (Diet 2), 100 g/kg (Diet 3), 150 g/kg (Diet 4) and 200 g/kg (Diet 5) to partially replace mainly soybean meal in triplicates. After 8 weeks feeding trial, the growth was significantly (P < 0.05) improved by dietary Ca P compared with the control. Whole-body crude lipid increased in the fish group fed over 50 g/kg Ca P (P < 0.05). Plasma triglycerides (TG) was significantly (P < 0.05) elevated by dietary Ca P protein at 200 g/kg. Ca P supplementation significantly (P < 0.05) up-regulated the mRNA expression of the growth-related insulin-like growth factor-1 (IGF-1). 50 g/kg and 100 g/kg dietary CaP improved the phosphorylation and protein levels of the eukaryotic initiation factor 4E binding protein 1 (4E-BP1) and ribosomal protein S6 Kinase 1 (S6K1), and the phosphorylation of the adenosine monophosphate-activated protein kinase (AMPK) compared with the control diet. The phosphorylation level of the phosphoinositide 3-kinase (PI3K) was lowered by 200 g/kg CaP compared with the control. The pyruvate kinase (PK) mRNA level was significantly (P < 0.05) up regulated by 100 g/kg CaP ; while glucose 6-phosphatase (G6Pase) mRNA expression was downregulated by 150 g/kg and 200 g/kg CaP compared with the control (P < 0.05). The mRNA expression of fatty acid transport protein 5 (FATP5) was significantly downregulated by 100- 200 g/kg; peroxisome proliferator-activated receptor alpha (PPARα) was significantly down-regulated by 50 g/kg; while fatty acid synthase (FAS) was significantly up-regulated by 150 g/kg and 200 g/kg CaP compared with the control (P < 0.05). The results further showed that GIFT juveniles fed with dietary CaP could regulate whole-body energy homeostasis through the AMPK signaling pathway. Therefore, Ca P could successfully be used as a novel and sustainable protein in juvenile GIFT diets.