Objectives To assess patients’ perceptions of continuity of care (COC) across primary care level and emergency departments (EDs) and to identify contextual and individual factors that influence this perception. Design Cross-sectional multicentre survey. Setting Five EDs in Brussels and Wallonia. Participants 501 adult patients referred to the ED by their primary care physician (PCP). Patients with cognitive impairment or in critical condition were excluded. Results Patients perceived high levels of the three types of COC. On an individual level, older patients showed a perception of higher levels of continuity. Lower levels of informational and management continuity were observed among patients suffering from chronic diseases and patients with a high level of education. Patients also perceived a redundancy of medical exams, in parallel to a high degree of accessibility between care levels. On an organisational level, three structural factors were identified as barriers to COC, namely, ED workload, suboptimal sharing information system and the current fee-for-service payment system that encourages competition and hinders coordination between actors. Conclusion Belgian healthcare services seem satisfying for patients and easily accessible. However, efforts need to be directed towards improving their efficiency. A stronger primary care level is also needed to benefit the healthcare system by reducing overuse of emergency services. On the individual level, a more enhanced patient-centred approach could be beneficial in improving patients experience of care.