To investigate the role of food source and energy control in the prevention and management of NAFLD, we conducted a systematic review and meta-analysis of controlled trials to assess the certainty of evidence for the effect of different food sources of fructose-containing sugars at different energy control levels on intrahepatocellular lipid (IHCL), as well as alanine aminotransferase (ALT), and aspartate aminotransferase (AST). This evidence concerns the gene GPT and metabolic dysfunction-associated steatotic liver disease.