Non-Alcoholic Fatty Liver Disease (NAFLD) is the main hepatic manifestations of metabolic syndrome. Some animal models of NAFLD are associated with dietary depletion of methyl donor substrates. The aim of this research was to study in adult rats the effect of dietary supplementation with promethylating substrates (betaine, choline, folic acid and vitamin B12) during different periods of life, on liver fat accumulation induced by a high-fat-sucrose (HFS) obesogenic dietary intake during adulthood, as well as the nutrigenomic and epigenomic mechanisms implicated in these processes. Animal models of obesity were achieved by HFS feeding, which were supplemented with a methyl donor cocktail to analyse the effect on adult male and female rats and the response to an obesogenic diet during adult life depending on perinatal maternal nutrition. In order to deepen into the mechanisms implicated we carried out magnetic resonance and plasma biochemical analysis, as well as transcriptomic (microarray and RT-qPCR) and DNA methylation-based techniques (mass spectrometry and radioactivity-related), among others. Obesogenic dietary intake was associated with an obese phenotype, while methyl donor supplementation decreased diet-induced liver fat accumulation. High-fat-sucrose diet intake and methyl donor supplementation showed changes on some plasma biochemical profile and on liver mRNA levels of genes related to obesity, lipid metabolism, liver injury or DNA methylation. Epigenetic features, as DNA methylation profile (both global and specific) were also characterized. Dietary supplementation with a promethylating cocktail prevented against high-fat-sucrose diet induced liver fat accumulation in rats. This protective effect is sex-independent and occurs by supplementing during adult life or after maternal intake during lactation. Hepatic transcriptome and epigenome are changed by obesogenic diet intake and by methyl donor dietary supplementation, affecting obesity (LepR), lipid metabolism (AcacA, Fasn, Srebf1, Srebf2, Agpat3), liver damage (Btc, Mme, Fat1) or DNA methylation (Dnmts) related genes.