Non-alcoholic fatty liver disease (NAFLD) encompassing a disease spectrum ranging from isolated steatosis to steatohepatitis (NASH) and fibrosis has become the most chronic liver disease worldwide. The pathophysiology of NAFLD is multifactorial, driven by insulin resistance and a sedentary lifestyle. In addition, gut microbiota and associated metabolites have been linked with NAFLD. The cornerstone treatment for NAFLD is lifestyle management but the evidence on the effect of exercise on advanced stages is not fully elucidated. Systematic literature search and meta-analyses were conducted to study the effect of exercise and diet therapy on NAFLD. The association of gut microbiota and physical activity was investigated in HELIUS cohort. The effect of exercise on liver histology and non-invasive parameters, such as magnetic resonance imaging (MRI) were investigated in patients with NAFLD in a 12-week high intensity interval training (HIIT). Tissue gene expression, gut microbiota composition and untargeted metabolomics, as well as gut motility in response to the exercise were investigated. Previous studies show that exercise alleviates steatosis but the evidence on advanced stages is contradictory. Gut microbiota is associated with physical activity. In the intervention study, HIIT in combination with home-based exercise improved cardiorespiratory fitness, and altered muscle mitochondrial metabolism of patients with NAFLD. HIIT did not ameliorate NAFLD as assessed on histology, MRI evaluation or liver function tests. Specific taxa and metabolites were significantly altered upon the exercise. The work warrants longer, and larger exercise interventions in patients with NAFLD to validate the present guidelines for exercise as cornerstone treatment for NAFLD.