Non-alcoholic fatty liver disease (NAFLD) is a challenge not only due to its rising prevalence but also, and perhaps more importantly, due to the lack of sustainable treatment options. Intestinal microbiota are thought to participate in the development and progression of NAFLD and their manipulation is, hence, being investigated as a treatment aim. This review summarizes the involvement of intestinal microbiota in the pathogenesis on NAFLD. In addition, we synthesize the results of the most recent animal and human studies aimed at treating dysbiosis seen in patients with NAFLD. Lastly, we review the evidence regarding the efficacy of manipulating short chain fatty acid and bile acid signaling in the treatment of NAFLD.