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Background: Disparities in vaccination coverage exist in Somalia with Internally Displaced Persons (IDPs) being among the groups with the lowest coverage. We implemented an adapted Participatory Learning and Action (PLA) intervention, which focused on routine vaccinations among displaced populations living in Mogadishu IDP camps. The intervention was successful in improving maternal knowledge and vaccination coverage but unsuccessful in improving timely vaccination. We conducted a qualitative study to understand this result and analyze the multi-level barriers to routine childhood immunization uptake. Method: In this qualitative study we used observation data from 40 PLA group discussions with female caregivers and purposively sampled nine vaccination service providers and six policy makers for interview. We also reviewed national-level vaccine policy documents and assessed the quality of health facilities in the study area. We used the socioecological framework to structure our analysis and analyzed the data in NVivo. Results: The barriers to childhood vaccination among IDPs at the individual level were fear due to lack of knowledge, mistrust of vaccines, concerns about side effects and misinformation; opportunity costs; and costs of transportation. At the interpersonal level, family members played an important role as did the extent of decision-making autonomy. Community factors such as cultural practices, gender roles, and household evictions influenced vaccination. Organizational issues at health facilities such as waiting times, vaccine stock-outs, distance to the facility, language differences, and hesitancy of health workers to open multi-dose vials affected vaccination. At the policy level, confusion about the eligible age for routine vaccination and age restrictions for catch-up vaccination and certain antigens such as BCG were important barriers. Conclusion: Complex and interrelated factors affect childhood vaccination uptake among IDPs in Somalia. Interventions that address multiple barriers simultaneously will have the greatest impact given the complex nature of vulnerabilities in this population. There is a need to strengthen the health system and connect it with existing community structures to increase demand for services. Our research highlights the importance of formative research before implementing interventions. Further research on the integration of health service strengthening with PLA to improve childhood vaccination among IDPs is recommended. Trial registration number: ISRCTN-83,172,390. Date of registration: 03/08/2021. [ABSTRACT FROM AUTHOR]