Background Across the world, 25–29% of the population suffer from pain. Pain is the most frequent reason for an emergency department (ED) visit. This symptom is involved in approximately 70% of all ED visits. The effective management of acute pain with adequate analgesia remains a challenge, especially for severe pain. Intravenous (IV) morphine protocols are currently indicated. These protocols are based on patient-reported scores, most often after an immediate evaluation of pain intensity at triage. However, they are not systematically prescribed. This aspect could be explained by the fact that physicians individualize opioid pain management for each patient and each care pathway to determine the best benefit–risk balance. Few data are available regarding bedside organizational factors involved in this phenomenon. Objective This study aimed to analyze the organizational factors associated with no IV morphine prescription in a standardized context of opioid management in a tertiary-care ED. Methods A 3-month prospective study with a case–control design was conducted in a French university hospital ED. This study focused on factors associated with protocol avoidance despite a visual analog scale (VAS) ≥60 or a numeric rating scale (NRS) ≥6 at triage. Pain components, physician characteristics, patient epidemiologic characteristics, and care pathways were considered. Qualitative variables (percentages) were compared using Fisher’s exact test or the chi-squared tests. Student’s t-test was used to compare continuous variables. The results were expressed as means with their standard deviation (SD). Factors associated with morphine avoidance were identified by logistic regression. Results A total of 204 patients were included in this study. A total of 46 cases (IV morphine) and 158 controls (IV morphine avoidance) were compared (3:1 ratio). Pain patterns and patient’s epidemiologic characteristics were not associated with an IV morphine prescription. Regarding NRS intervals, the results suggest a practice disconnected from the patient’s initial self-report. IV morphine avoidance was significantly associated with care pathways. A significant difference between the IV morphine group and the IV morphine avoidance group was observed for “self-referral” [adjusted odds ratio (aOR): 5.11, 95% CIs: 2.32–12.18, p < 0.0001] and patients’ trajectories (Fisher’s exact test; p < 0.0001), suggesting IV morphine avoidance in ambulatory pathways. In addition, “junior physician grade” was associated with IV morphine avoidance (aOR: 2.35, 95% CIs: 1.09–5.25, p = 0.03), but physician gender was not. Conclusion This bedside case–control study highlights that IV morphine avoidance in the ED could be associated with ambulatory pathways. It confirms the decreased choice of “NRS-only” IV morphine protocols for all patients, including non-trauma patterns. Modern pain education should propose new tools for pain evaluation that integrate the heterogeneity of ED pathways.