Introduction Coeliac disease (CD) affects 1% of the population worldwide. The only available evidence-based treatment is a strict gluten-free diet (GFD), which can readily lead to weight gain and unfavourable metabolic changes (eg, dyslipidaemia, fatty liver disease and insulin resistance) if followed without adequate dietary control. That can lead to increased cardiovascular risk (CV). We planned a randomised controlled trial to test the effect of a group-based, structured, 1-year, advanced dietary education, per the proposal of a Mediterranean diet vs standard of care, regarding the most relevant CV risk factors (eg, metabolic parameters and body composition) in CD patients. Methods and analysis Randomisation will occur after the baseline dietary education and interview in a 1:1 allocation ratio. Outcomes include anthropometric parameters (body composition analysis including weight, Body Mass Index, fat mass, per cent body fat, skeletal muscle mass, visceral fat area and total body water) and CV risk-related metabolic parameters (eg, lipid profile, homocysteine, fasting glucose, haemoglobin A1c, Homeostatic Model Assessment Index, metabolic hormones, waist circumference, blood pressure, liver function tests, liver steatosis rate and diet composition). In this study, we aim to draw attention to a new aspect regarding managing CD: dietary education can lead to a better quality of the GFD, thereby reducing the risk of potential metabolic and CV complications. Ethics and dissemination The study was approved by the Scientific and Research Ethics Committee of the Hungarian Medical Research Council (27521-5/2022/EÜIG). Findings will be disseminated at research conferences and in peer-reviewed journals. Trial registration number NCT05530070