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Introduction Metabolic syndrome (MetS) is a cluster of cardio-metabolic dysfunctions characterised by increased fasting plasma glucose, waist circumference, blood pressure, triglycerides and reduction in high-density lipoprotein cholesterol. Meanwhile, metabolic dysfunction-associated fatty liver disease (MAFLD) is the new term for fatty liver associated with MetS. People with MetS or MAFLD have higher risks for adverse cardiovascular outcomes and mortalities. However, large-scale data on MetS and MAFLD prevalence in Malaysia is mainly unknown. This study aims to determine the prevalence of MetS and MAFLD among the general adult population in Malaysia.Methods and analysis This is a community-based nationwide cross-sectional study in Malaysia. The data collection period is from July 2023 until September 2023, with a planned sample size of 1296 participants. We use a two-stage proportionate stratified random sampling method to ensure national representativeness. The definition of MetS follows the Harmonised Joint Interim Statement in 2009. A diagnosis of MAFLD is made if a participant has fatty liver, defined as having a Fatty Liver Index ≥60 and has type 2 diabetes, a body mass index ≥23 kg/m2, or ≥2 metabolic risk abnormalities. Complex sample analysis will be conducted, and the disease prevalence will be reported with 95% CIs, unweighted counts and estimated populations.Ethics and dissemination The protocol has been approved by the Medical Research and Ethics Committee of the Ministry of Health Malaysia (NMRR ID-22–02845-GUT). The findings will be disseminated through a formal report, policy brief, scientific publications, conference presentations, social media, print media and stakeholder engagement activities.