Implementation science scholars argue that knowing ‘what works’ in public health is insufficient to change practices, without understanding ‘how’, ‘where’ and ‘why’ something works. In the peer reviewed literature on conflict-affected settings, challenges to produce research, make decisions informed by evidence, or deliver services are documented, but what about the understanding of ‘how’, ‘where’ and ‘why’ changes occur? We explored these questions through a scoping review of peer-reviewed literature based on core dimensions of the Extended Normalization Process Theory. We selected papers that provided data on how something might work (who is involved and how?), where (in what organizational arrangements or contexts?) and why (what was done?). We searched the Global Health, Medline, Embase databases. We screened 2054 abstracts and 128 full texts. We included 22 papers (of which 15 related to mental health interventions) and analysed them thematically. We had the results revised critically by co-authors experienced in operational research in conflict-affected settings. Using an implementation science lens, we found that: (a) implementing actors are often engaged after research is produced to discuss feasibility; (b) new interventions or delivery modalities need to be flexible; (c) disruptions affect how research findings can lead to sustained practices; (d) strong leadership and stable resources are crucial for frontline actors; (e) creating a safe learning space to discuss challenges is difficult; (f) feasibility in such settings needs to be balanced. Lastly, communities and frontline actors need to be engaged as early as possible in the research process. We used our findings to adapt the Extended Normalization Process Theory for operational research in settings affected by conflicts. Other theories used by researchers to document the implementation processes need to be studied further.