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Lifestyle interventions remain the first-line therapy for nonalcoholic fatty liver disease (NAFLD). This study aims to evaluate the individual impact of exercise and/or dietary interventions on the level of alanine aminotransferase (ALT), aspartate aminotransferase (AST), homeostasis model of assessment for insulin resistance index (HOMA-IR), and BMI. Randomized-controlled trials from patients diagnosed with NAFLD were included in the meta-analysis if they reported the associations between changes in ALT, AST, HOMA-IR, or BMI and types of lifestyle interventions. Nineteen eligible articles were included. Compared with observation, aerobic exercise training (AEx) plus diet [weighted mean difference (WMD)=−25.85; 95% confidence interval (CI): −43.90 to −7.80], AEx (WMD=−8.81; 95% CI: −20.22–2.60) and diet (WMD=−11.85; 95% CI: −47.65–24.95) showed significant efficacy in the improvement of ALT levels. Also AST, AEx plus diet showed a significant tendency to reduce AST levels. In addition, progressive resistance training (WMD=−1.70; 95% CI: −5.61–2.21) led to the most obvious reduction in HOMA-IR compared with observation, but appeared to show no significant effect in BMI (WMD=0.27; 95% CI: −0.48 to −0.07), whereas AEx plus diet (WMD=−0.96; 95% CI: −1.54 to −0.38 and WMD=−1.96; 95% CI: −2.79 to −1.12) showed great efficacy both in the improvement of HOMA-IR and BMI. AEx plus diet is the most effective intervention in the management of patients with NAFLD. Dietary intervention may be more effective in the improvements of aminotransferases, whereas exercise shows superiority in improving insulin sensitivity and reduction of BMI.