Background and aims <p>In recent years, the prevalence of non-alcoholic fatty liver disease (NAFLD) has risen among patients with chronic hepatitis B (CHB), coinciding with the increasing rates of obesity and metabolic syndrome. Both conditions can contribute to liver fibrosis and even hepatocellular carcinoma; however, the pathogenesis of each disease, as well as CHB concurrent with NAFLD, remains incompletely understood.</p> Methods <p>We comprehensively analyzed protein levels in liver tissues from four distinct groups: healthy controls, patients with CHB, patients with NAFLD, and those with CHB and NAFLD using proteomic profiling. Subsequently, we performed bioinformatics analyses based on the results of differentially expressed proteins (DEPs). We also verified the levels of select DEPs in both patient liver samples and a murine model.</p> Results <p>Our investigation revealed that enhanced viral clearance in patients with hepatitis B virus (HBV) with concurrent NAFLD might be associated with an inflammatory response and the activation of numerous metabolic pathways within the body. Meanwhile, the degree of hepatic steatosis was associated with anomalies in fatty acid degradation, glycolysis/gluconeogenesis, and other metabolic processes. However, the prognosis for patients with CHB and concurrent NAFLD may be severe, and this may be connected to the altered levels of proteins such as ACAT1, ACY1, SERPINB3, MTCH2, ALDH2, ECHS1, S100A7, and LRP6.</p> Conclusion <p>In comparison to CHB and NAFLD alone, the prognosis for CHB complicated by NAFLD appears less favorable. This disparity is closely correlated with distinct protein level patterns in the liver following the onset of both diseases. Our study provides novel insights into the disease progression and clinical mechanisms underlying CHB and NAFLD.</p>