Background The health benefits of physical exercise have been shown to be important in the prevention of cardiovascular diseases in patients with hypertension, dyslipidaemia or diabetes. However, few strategies have demonstrated efficacy and practicality in the promotion of physical exercise among this group of patients in general practice. Methods The PEPPER clinical study is a randomised controlled trial to evaluate the efficacy over a period of 12 months, in terms of physical activity level, of an intervention based on structured information delivery, a personalised written physical activity prescription in number of steps per day, a pedometer and a pedometer logbook, in 35 to 74-year-old patients with cardiovascular risk factors. 140 patients will be recruited in 15 GP practices and randomised in the intervention group or in the control group where patients will receive verbal advice of physical exercise. The primary outcome is the change at three months in total energy expenditure measured by an accelerometer over a 7-day period. Secondary outcomes include changes at 3 and 12 months in physical activity levels (accelerometer and International Physical Activity Questionnaire), quality of life (SF-36), blood pressure, weight, waist circumference, perceived obstacles to physical activity and patient compliance with the recommended strategy. Both groups will be compared using mixed models. Discussion The results are expected at the end of 2019. If the intervention proves effective in durably increasing the level of physical activity, this strategy could be tested in a larger trial to examine its impact on cardiovascular diseases. Trial registration US National Institutes of Health Clinical Trials Registry NCT02317003 , December 15, 2014.