This study aimed to assess the effect of quercetin when administered orally complexed with HP-β-CD in the form of Que-HP-β-CD lyophilized product on NAFLD and to explore the role of key autophagy-related proteins (Beclin1, p62, LC3A, and LC3B), in the disease’s progression and potential therapeutic modulation. This evidence concerns the gene MAP1LC3B and metabolic dysfunction-associated steatotic liver disease.