Despite recent advances in running shoe conception, injuries represent a major concern in the running community. The objective of this study was to gather the pilot data for a larger randomised controlled trial regarding the effects of traditional and minimalist shoes on the incidence of running-related injuries (RRI), as well as the rate of adherence to a running programme. Twenty-six recreational runners were recruited. They were randomly assigned to minimalist (MS) or traditional (TS) shoes and participated in a 16-week training programme. The information on previously reported risk factors for RRI was gathered. Participants reported pain and compliance using an online tool. Main outcome measures included the rates of recruitment, adherence to the programme and programme completion, RRI and the missed training days secondary to the running-related pain. The recruited runners represented 72.2% of potential participants, among which 20 (76.9%) completed the programme. Two subjects dropped out before randomisation, plus three in MS and one in TS during the programme. Rate of adherence was 82.4% in MS and 86.2% in TS. Three runners per group sustained an RRI (25%, 95% C.I. = 9.8%–46.7%). Results support the feasibility of a larger scale study. A total of 116 runners would be needed to detect a clinically significant difference of 20% in injury incidence between MS and TS.