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Background Trauma-focused psychological interventions are central to treating PTSD and CPTSD among trauma-affected refugees, yet it remains unclear how patient-reported outcome measures (PROMs) can be meaningfully implemented in high-complexity clinical settings. This study examined real-world use of a web-based PROM system embedded in routine care for trauma-affected refugees in Denmark. Methods We conducted a convergent, embedded mixed-methods case study at a specialist outpatient clinic participating in the Danish Trauma Database for Refugees (DTD). Quantitative data comprised (a) system-generated flow data for all patients referred between February 2023 and August 2025 (N = 634), describing registration, consent, and assessment completion at baseline, end of treatment, and 6-month follow-up, and (b) a clinician survey on usability and clinical value (n = 15). Qualitative data consisted of 10 semi-structured interviews with two clinician–patient dyads conducted at baseline, mid-treatment, and post-treatment, analyzed using reflexive thematic analysis. Findings were integrated across data sources to address implementation, perceived usability, experiences of use, and how these perspectives intersect. Results Of 634 registered patients, 270 (42%) provided active research consent. Baseline PROM completion was moderate, with most patients contributing at least partial data, whereas completion declined substantially at post-treatment and follow-up (e.g., 77% and 90% of assessments unregistered, respectively). Clinicians rated technical usability as acceptable but reported limited perceived impact on clinical insight, personalized care, and interdisciplinary collaboration; half expressed concern that research demands risked overshadowing clinical priorities. Qualitative analyses identified three overarching themes: (1) the therapeutic relationship as the primary outcome, with PROMs secondary to being heard and recognized; (2) PROMs as routinised yet relationally negotiated tools, used mainly at intake; and (3) ongoing tension between standardization and flexibility as clinicians adapted PROM use to patients’ capacities and perceived vulnerability. Conclusion In this trauma-focused refugee service, PROMs were only partially implemented and mainly used at baseline. Barriers were primarily epistemic and ethical rather than technical, reflecting concerns about clinical relevance, workflow fit, and protection of “vulnerable” patients. Sustainable PROM implementation in such settings likely requires co-created, reflexive approaches that prioritize epistemic fit, relational care, and proportionate inclusion over procedural compliance.