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Introduction Being physically active is associated with a wide range of health benefits in patients. However, many patients do not engage in the recommended levels of physical activity (PA). To date, interventions promoting PA in patients mainly rely on providing knowledge about the benefits associated with PA to develop their motivation to be active. Yet, these interventions focusing on changing patients' conscious goals have proven to be rather ineffective in changing behaviours. Recent research on automatic factors (eg, automatic approach tendencies) may provide additional targets for interventions. However, the implementation and evaluation of intervention designed to change these automatic bases of PA are rare. Consequently, little is known about whether and how interventions that target automatically activated processes towards PA can be effective in changing PA behaviours. The Improving Physical Activity (IMPACT) trial proposes to fill this knowledge gap by investigating the effect of a cognitive-bias modification intervention aiming to modify the automatic approach towards exercise-related stimuli on PA among patients. Methods and analysis The IMPACT trial is a single-centre, placebo (sham controlled), triple-blinded, phase 3 randomised controlled trial that will recruit 308 patients enrolled in a rehabilitation programme in the Division of General Medical Rehabilitation at the University Hospital of Geneva (Switzerland) and intends to follow up them for up to 1 year after intervention. Immediately after starting a rehabilitation programme, patients will be randomised (1:1 ratio) to receive either the cognitive-bias modification intervention consisting of a 12-session training programme performed over 3 weeks or a control condition (placebo). The cognitive-bias modification intervention aims to improve PA levels through a change in automatic approach tendencies towards PA and sedentary behaviours. The primary outcome is the sum of accelerometer-based time spent in light-intensity, moderate-intensity and vigorous-intensity PA over 1 week after the cognitive-bias modification intervention (in minutes per week). Secondary outcomes are related to changes in (1) automatic approach tendencies and self-reported motivation to be active, (2) physical health and (3) mental health. Sedentary behaviours and self-reported PA will also be examined. The main time point of the analysis will be the week after the end of the intervention. These outcomes will also be assessed during the rehabilitation programme, as well as 1, 3, 6 and 12 months after the intervention for secondary analyses. Ethics and dissemination The study will be conducted in accordance with the Declaration of Helsinki. This trial was approved by the Ethics Committee of Geneva Canton, Switzerland (reference number: CCER2019-02257). All participants will give an informed consent to participate in the study. Results will be published in relevant scientific journals and be disseminated in international conferences. Trial registration details The clinical trial was registered at the German clinical trials register (reference number: DRKS00023617); Pre-results.