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Introduction Metabolic associated fatty liver disease (MAFLD) is internationally prevalent, resulting in considerable health and economic costs. Lifestyle adjustments, especially exercise, constitute fundamental treatments; nonetheless, sustained adherence poses significant challenges. This study is to assess the effectiveness of a 12-week digital exercise intervention in decreasing liver fat and enhancing metabolic outcomes in individuals with MAFLD.Methods and analysis This pragmatic, investigator-initiated study is a stratified, randomised controlled parallel-group clinical trial. Participants meeting the enrolment criteria will be stratified and randomised based on exercise habits and risk levels. They will be allocated into either the intervention group or the active-control group,with 50 participants per group. Participants in the intervention group will undergo a 12-week digital platform-based exercise intervention customised to their activity risk classification, encompassing exercise monitoring, dietary intervention and health education. Simultaneously, the active-control group will receive traditional exercise monitoring, dietary intervention and health education after the development of their health plan. The primary outcome measure will be liver fat fraction measured by magnetic resonance imaging-proton density fat fraction. Secondary outcome measures will encompass body composition, blood pressure, body weight, body mass index, blood lipids, liver function and additional factors. Evaluations will be performed at baseline and after the intervention (12 weeks).Ethics and dissemination Ethical approval of this trial was granted by the ethics committee of the First Affiliated Hospital of Nanjing Medical University (2024-SR-167). Informed written consent will be acquired from study participants prior to enrolment. The results will be published in peer-reviewed journals.Trial registration number ChiCTR2400083477.