Adverse events occur frequently at emergency departments (ED) because of several risk factors related to varying conditions. It is still unclear, which factors lead to patient safety incident reports. The aim of this study was to explore the root causes behind ED-associated patient safety incidents reported by personnel, and based on the findings, to suggest learning objectives for improving patient safety. The study material included incident reports (n = 340) which concerned the ED of a teaching hospital over one year. We used a mixed method combining quantitative descriptive statistics and qualitative research by inductive content analysis and deductive Ishikawa root cause analysis. Most (76.5%) incidents were reported after patient transfer from the ED. Nurses reported 70% of incidents and physicians 7.4%. Of the reports,40% were related to information flow or management. Incidents were evaluated as no harm (29.4%), mild (46%), moderate (19.7%), and severe (1.2%) harm to the patient. The main consequences for the organization were reputation loss (44.1%) and extra work (38.9%). In the qualitative analysis, nine specific problem groups were found: insufficient introduction, adherence to guidelines and protocols, insufficient human resources, deficient professional skills, medication management deficiencies, incomplete information transfer from the ED, language proficiency, unprofessional behaviour, identification error, and patient-dependent problems. Six organizational themes were identified: medical staff orientation, onboarding and competence requirements; human resources; electronic medical records and information transfer; medication documentation system; interprofessional collaboration; resources for specific patient groups such as geriatric, mental health, and patients with substance abuse disorder. Entirely human factor-related themes could not be defined because their associations with system factors were complex and multifaceted. Individual and organizational learning objectives were addressed, such as adherence to the proper use of instructions and adequate onboarding. System factors caused most of the patient safety incidents reported concerning ED. The introduction and training of ED -processes is elementary, as is multiprofessional collaboration. More research is needed about teamwork skills, patients with special needs and non-critical patients, and the reporting of severe incidents.