Background Current management of patients with atrial fibrillation (AF) is limited by low detection of AF, non-adherence to guidelines and lack of consideration of patient's preferences, thus highlighting the need for a holistic and integrated approach to AF management. This study aims to determine whether a mHealth technology-supported AF integrated management strategy will reduce AF-related adverse events. Methods/design The mAFA II trial is a prospective, cluster randomised controlled trial. The 40 sites will be randomised to mAFA-integrated care intervention or usual care arms. Prior to randomisation, study sites will be paired to be matched in size and the proportion of study eligible patients. All AF patients aged over 18 years old with CHA(2)DS(2)-VASc score >= 2 will be enrolled. Assuming a composite adverse event rate of 10% pre-intervention, reduced to 5% after intervention, we aim to recruit 3660 patients assuming a 10% loss to follow-up. The primary study endpoint is a composite of stroke/thromboembolism, all-cause death and rehospitalisation. Ancillary analyses would determine patient-related outcome measures, health economics and cost effectiveness, as well as an embedded qualitative study. Discussion The mAFA II trial will provide evidence for an integrated care approach to holistic AF care, supported by mobile health technology to improve screening, patient involvement and optimisation of management.