Abstract Background Decision Boxes are summaries of the most important benefits and harms of health interventions provided to clinicians before they meet the patient, to prepare them to help patients make informed and value-based decisions. Our objective is to explore the barriers and facilitators to using Decision Boxes in clinical practice, more precisely factors stemming from (1) the Decision Boxes themselves, (2) the primary healthcare team (PHT), and (3) the primary care practice environment. Methods/design A two-phase mixed methods study will be conducted. Eight Decision Boxes relevant to primary care, and written in both English and in French, will be hosted on a website together with a tutorial to introduce the Decision Box. The Decision Boxes will be delivered as weekly emails over a span of eight weeks to clinicians of PHTs (family physicians, residents and nurses) in five primary care clinics located across two Canadian provinces. Using a web-questionnaire, clinicians will rate each Decision Box with the Information Assessment Method (cognitive impacts, relevance, usefulness, expected benefits) and with a questionnaire based on the Theory of Planned Behavior to study the determinants of clinicians’ intention to use what they learned from that Decision Box in their patient encounter (attitude, social norm, perceived behavioral control). Web-log data will be used to monitor clinicians’ access to the website. Following the 8-week intervention, we will conduct semi-structured group interviews with clinicians and individual interviews with clinic administrators to explore contextual factors influencing the use of the Decision Boxes. Data collected from questionnaires, focus groups and individual interviews will be combined to identify factors potentially influencing implementation of Decision Boxes in clinical practice by clinicians of PHTs. Conclusions This project will allow tailoring of Decision Boxes and their delivery to overcome the specific barriers identified by clinicians of PHTs to improve the implementation of shared decision making in this setting.