IntroductionLifestyle interventions targeting weight loss and improved dietary patterns are the recommended treatment for non-alcoholic fatty liver disease (NAFLD). However, the effectiveness of current established diet therapies is suboptimal. The patatin‐like phospholipase domain containing 3 (PNPLA3) gene modifies disease outcome and hepatic lipid handling, but the role of PNPLA3 variants in modulating responsiveness to different diet therapies is unknown.Methods and analysisThis project aims to assess the feasibility of conducting a genotype-driven randomised controlled trial (RCT) investigating the differential response to a Mediterranean diet (MD) intervention of NAFLD patients according to genotype for the rs738409 (I148M) variant of PNPLA3. A single-centre randomised controlled feasibility trial will be undertaken. We will recruit 60 adults with NAFLD from a tertiary hepatology centre in England. In a cross-over design, participants will undertake Diet 1 (MD) and Diet 2 (control) for 4 weeks, in random order (1:1 allocation), separated by a 4 weeks washout period. Participants will complete one-to-one diet and lifestyle consultations at baseline, end of diet phase 1, end of washout and end of diet phase 2. Participants will be advised to maintain baseline levels of physical activity and body weight. The primary outcome is the acceptability and feasibility of the intervention protocol. Secondary outcomes include exploratory assessment of liver fibrosis biomarkers and lipid biomarkers.Ethics and disseminationEthical approval was granted by East of Scotland Research Ethics Service REC 1 (19/ES/0112). Results will be disseminated through peer-reviewed journals and presented at local, national and international meetings and conferences. The findings of this trial will lay the foundation for a future definitive RCT by informing trial design and optimising the intervention diets, instruments and procedures.Trial registration numberISRCTN93410321.