In conflict settings, research capacities have often been de-prioritized as resources are diverted to emergency needs, such as addressing elevated morbidity, mortality and health system challenges directly and/or indirectly associated to war. This has had an adverse long-term impact in such protracted conflicts such as those found in the Middle East and North Africa region (MENA), where research knowledge and skills have often been compromised. This paper proposes a conceptual framework for health research capacity strengthening that adapts existing models and frameworks in low- and middle-income countries and uses the knowledge of the MENA context to contextualise them for conflict settings.