Background The conflict in Yemen has devastated the health system, with only 51% of health facilities classified as fully functional and 19.7 million people lacking access to health care. To address the urgent need for primary health care services in rural communities, Save the Children launched an iCCM program in Lahj and Taiz Governorates. A qualitative study was conducted to document the challenges to iCCM service delivery and to aid in developing strategies for overcoming service delivery bottlenecks in conflict-affected rural areas. Methods Qualitative data were collected in Aden City, Lahj Governorate, and Taiz Governorate. Twenty-three IDIs and six FGDs were conducted with iCCM stakeholders at all levels. Results Key findings included: 1) Policy, coordination, and funding were challenged by the fact that iCCM was not integrated into the national health system and was implemented as a short-term emergency program. 2) Villages that received services from a CHW who was based in a different community experienced reduced access to services, especially during times of heightened conflict and insecurity, when CHWs could not travel. 3) Supervision, supply chain, and monitoring were all challenges that were exacerbated by difficulties in travel due to the conflict. Potential solutions to these included the use of mobile technology for supervision and data collection and pre-positioning of buffer stocks in locations closer to CHWs. 4) Travel was seen as the primary threat to the safety of CHWs and supervisors. Measures taken to reduce the risk included limiting travel during periods of heightened insecurity, safety training for CHWs, and use of mobile technology for communication. Conclusions CHWs were able to provide iCCM services in a challenging and insecure context. The challenges in delivery of services were related to both a weak health system and the conflict. Several adaptations to service delivery to overcome the bottlenecks have been identified and should be considered for future community health programs. The closure of the program in Taiz after only 14 months of implementation is a stark illustration of the failure of the current model of short-term humanitarian funding to address long-term needs in protracted emergencies.