Introduction Adults with lower levels of health literacy are less likely to engage in health-promoting behaviours. Our trial evaluates the impacts and outcomes of a mobile health-enhanced preventive intervention in primary care for people who are overweight or obese. Methods and analysis A two-arm pragmatic practice-level cluster randomised trial will be conducted in 40 practices in low socioeconomic areas in Sydney and Adelaide, Australia. Forty patients aged 40-70 years with a body mass index ≥28 kg/m 2 will be enrolled per practice. The HeLP-general practitioner (GP) intervention includes a practice-level quality improvement intervention (medical record audit and feedback, staff training and practice facilitation visits) to support practices to implement the clinical intervention for patients. The clinical intervention involves a health check visit with a practice nurse based on the 5As framework (assess, advise, agree, assist and arrange), the use of a purpose-built patient-facing app, my snapp, and referral for telephone coaching. The primary outcomes are change in health literacy, lifestyle behaviours, weight, waist circumference and blood pressure. The study will also evaluate changes in quality of life and health service use to determine the cost-effectiveness of the intervention and examine the experiences of practices in implementing the programme. Ethics and dissemination The study has been approved by the University of New South Wales (UNSW) Human Research Ethics Committee (HC17474) and ratified by the University of Adelaide Human Research Ethics committee. There are no restrictions on publication, and findings of the study will be made available to the public via the Centre for Primary Health Care and Equity website and through conference presentations and research publications. Deidentified data and meta-data will be stored in a repository at UNSW and made available subject to ethics committee approval. Trial Registrationregistration number ACTRN12617001508369; Pre-results.