INTRODUCTION: Short-term exercise prehabilitation programmes have demonstrated promising results in improving aerobic capacity of unfit patients prior to major abdominal surgery. However, little is known about the cardiac and skeletal muscle adaptations explaining the improvement in aerobic capacity following short-term exercise prehabilitation. METHODS AND ANALYSIS: In this single-centre study with a pretest-post-test design, 12 unfit patients with a preoperative oxygen uptake (VO2) at the ventilatory anaerobic threshold ≤13 mL/kg/min and/or VO2 at peak exercise ≤18 mL/kg/min, who are scheduled to undergo hepatopancreatobiliary surgery at the University Medical Center Groningen (UMCG), the Netherlands, will be recruited. As part of standard care, unfit patients are advised to participate in a home-based exercise prehabilitation programme, comprising high-intensity interval training and functional exercises three times per week, combined with nutritional support, during a 4-week period. Pre-intervention and post-intervention, patients will complete a cardiopulmonary exercise test. Next to this, study participants will perform additional in-vivo exercise cardiac magnetic resonance (MR) imaging and phosphorus 31-MR spectroscopy of the quadriceps femoris muscle before and after the intervention to assess the effect on respectively cardiac and skeletal muscle function. ETHICS AND DISSEMINATION: This study was approved in May 2023 by the Medical Research Ethics Committee of the UMCG (registration number NL83611.042.23, March 2023) and is registered in the ClinicalTrials.gov register. Results of this study will be submitted for presentation at (inter)national congresses and publication in peer-reviewed journals. TRIAL REGISTRATION NUMBER: NCT05772819.