Non-alcoholic fatty liver disease (NAFLD) is a most important cause of liver disease. Similar to other non-communicable diseases (NCD), such as obesity and type II diabetes mellitus, NAFLD can strongly affected by diet. Diet-related NCD and malnutrition are rising in all regions being a major cause of the global health, economic and environmental burdens. Mushrooms, important dietary components since the hunter-gathering communities, have increasingly gained momentum in biomedical research and therapeutics due to their interplay in metabolism traits. We emphasize here the beneficial effects of mushroom-enriched diets on the homeostasis of lipid and sugar metabolism, including their modulation, but also interfering with insulin metabolism, gut microbiota, inflammation, oxidative stress and autophagy. In this review, we describe the cellular and molecular mechanisms at the gut-liver axis and the liver-white adipose tissue (WAT) axis, that plausibly cause such positive modulation, and discuss the potential of mushroom-enriched diets to prevent or ameliorate NAFLD and related NCD, also within the shift needed toward healthy sustainable diets.