Abstract Background Continuing medical education (CME), as a systematic attempt to facilitate change in General Practitioners’ (GPs) practices, is considered crucial, assuming that if physicians are up-to-date, they will change and improve their practice, resulting in better performance and ultimately better patient care. However, studies continue to demonstrate considerable gaps between the real and ideal performance and patient-related outcomes. The objective of this study was to explore GP’s perception of the factors affecting the implementation of a CME digital platform in a primary health care setting in Portugal. Methods Our work is framed in a larger effectiveness-implementation hybrid type 1 study, where a Digital Behaviour Change Intervention (DBCI), called ePrimaPrescribe, was developed and implemented with the aim of changing benzodiazepines (BZD) prescribing patterns. Our design used mixed methodologies to obtain an enriched knowledge on GPs’ perspectives on the facilitators and barriers to implementing a Digital Behaviour Change Intervention (DBCI) applied to CME. To do so, we used data coming from an onsite questionnaire, an adapted version of the Barriers and Facilitators Assessment Instrument (BaFAI) and in-depth interviews. Results From the 47 GPs successfully included in the intervention arm of our cluster-randomized effectiveness study, we collected 37 onsite questionnaires, 24 BaFAIs, and performed 12 in-depth interviews. GPs reported as the main barriers to CME a lack of time, a perception of work overload, a lack of digital competence, a lack of digital infrastructure, and motivational and emotional factors. They reported as facilitators to CME delivered through a DBCI the convenience of the delivery method, the practical and pragmatic characteristics of the content, and the possibility for CME to be mandatory. Conclusions The perceptions of the barriers and facilitators reported by GPs represent an important contribution to improving knowledge regarding the factors influencing the implementation of CME in primary health care settings. We consider that our study might bring useful insights to other countries where primary health care plays a central role in the provision of care. Trial registration ClinicalTrials.gov number NCT04925596.