Background: Modern diets, characterised by excess consumption of processed foods, are accompanied by an epidemic of chronic diseases. Cardiovascular disease and depression carry a large burden of disease and often occur together. Poor dietary patterns have been identified as an independent risk factor for depression while healthy diets with minimally processed food are protective. Traditional Mediterranean diets have been shown to reduce risk of cardiovascular disease; however there is a need for clinical trials in people with depression. This paper reports the study protocol of a Mediterranean-style diet intervention conducted in adults with self-reported depression. Methods/design: HELFIMED is a parallel 6-month randomised controlled trial investigating whether dietary patterns can be improved in people with depressive symptoms and whether healthier diet combined with fish oil supplementation can improve mental and cardiometabolic health and quality of life. Adults aged 18-65 years with self-reported depressive symptoms over the previous two months (N = 163) were block-randomised on age and gender between May 2014 and June 2015 to receive nutrition education, food hampers, fortnightly cooking workshops based on Mediterranean-style dietary principles for 3 months and fish oil supplementation for 6 months, or to attend fortnightly social groups (control group) for 3 months. All participants completed mental health (DASS and PANAS), quality of life, dietary and shopping and budgeting questionnaires and provided anthropometric measurements, blood and urine samples at baseline, 3 and 6 months. Additionally the treatment group attended focus groups at 3 and 6 months. Primary and secondary outcomes will be analysed using linear mixed modelling and correlations will investigate associations between improved health outcomes and subjective/objective measures of improved diet/nutritional status. Discussion: This study will contribute causal evidence to prior observational and longitudinal studies that have shown associations between Mediterranean diet and mental health. The results will inform public health and clinical strategies for treatment of depression and comorbid cardiometabolic risk factors. Trial registration: Australian New Zealand Clinical Trials Register (ACTRN12614000438651). Trial registration date: 23rd April 2014.