Several indicators reflect the quality of care within emergency departments (ED). The length of stay (LOS) of emergency patients represents one of the most important performance measures. Determinants of LOS have not yet been evaluated in large cohorts in Germany. This study analyzed the fixed and influenceable determinants of LOS by evaluating data from the German Emergency Department Data Registry (AKTIN registry). We performed a retrospective evaluation of all adult (age ≥ 18 years) ED patients enrolled in the AKTIN registry for the year 2019. Primary outcome was LOS for the whole cohort; secondary outcomes included LOS stratified by (1) patient-related, (2) organizational-related and (3) structure-related factors. Overall, 304,606 patients from 12 EDs were included. Average LOS for all patients was 3 h 28 min (95% CI 3 h 27 min–3 h 29 min). Regardless of other variables, patients admitted to hospital stayed 64 min longer than non-admitted patients. LOS increased with patients’ age, was shorter for walk-in patients compared to medical referral, and longer for non-trauma presenting complaints. Relevant differences were also found for acuity level, day of the week, and emergency care levels. We identified different factors influencing the duration of LOS in the ED. Total LOS was dependent on patient-related factors (age), disease-related factors (presentation complaint and triage level), and organizational factors (weekday and admitted/non-admitted status). These findings are important for the development of management strategies to optimize patient flow through the ED and thus to prevent overcrowding.