A healthy diet provides a favourable environment that allows the essential bacteria to grow and ferment beneficial metabolites, short-chain fatty acids (SCFA) through various metabolic pathways. SCFA, including linear- and branched-SCFA (BSCFA) are important in regulating energy haemostasis, inflammation, and appetite. A plant-based diet is associated with increased SCFA levels and SCFA-producing bacteria that regulate nutrient metabolism. Conversely, an animal-based diet is associated with lower SCFA levels and its producing bacteria. The Malaysian dietary guidelines are in line with other healthy eating recommendations that promote vegetables and fruit intake. Very few clinical studies are available to explore the association of gut microbiota and SCFA profiles following a Malaysian diet and the detailed amount of oil consumption was not reported. The available data demonstrated that acetate, propionate, and butyrate were the most abundant SCFA, while BSCFA, isobutyrate, was less abundant in Malaysian. Firmicutes and Bacteroidetes are the predominant phyla, while Faecalibacterium and Prevotella are the dominant SCFA-producing genera in Malaysian. Prevotella is associated with metabolic pathways for carbohydrates and fatty acids. However, more long-term cohort studies are needed to further elucidate the association between gut microbiota composition, SCFA profiles and the potential health effects of palm oil consumption in Malaysian diet.