Mexico is going through an environmental and nutritional crisis related to unsustainable dietary behaviours. Sustainable diets could solve both problems together. This study protocol aims to develop a three-stage, 15-week mHealth randomised controlled trial of a sustainable-psycho-nutritional intervention programme to promote Mexican population adherence to a sustainable diet and to evaluate its effects on health and environmental outcomes. In stage 1, the programme will be designed using the sustainable diets, behaviour change wheel and capability, opportunity, motivation, and behaviour (COM-B) models. A sustainable food guide, recipes, meal plans and a mobile application will be developed. In stage 2, the intervention will be implemented for 7 weeks, and a 7-week follow-up period in a young Mexican adults (18–35 years) sample, randomly divided (1:1 ratio) into a control group (n 50) and an experimental group (n 50), will be divided into two arms at week 8. Outcomes will include health, nutrition, environment, behaviour and nutritional-sustainable knowledge. Additionally, socio-economics and culture will be considered. Thirteen behavioural objectives will be included using successive approaches in online workshops twice a week. The population will be monitored using the mobile application consisting of behavioural change techniques. In stage 3, the effects of the intervention will be assessed using mixed-effects models on dietary intake and quality, nutritional status, physical activity, metabolic biomarkers (serum glucose and lipid profile), gut microbiota composition and dietary water and carbon footprints of the evaluated population. Improvements in health outcomes and a decrease in dietary water and carbon footprints are expected.