Background Reducing Ebola virus transmission relies on the ability to limit contact with infected bodily fluids through biosecurity, safe sex practices, safe burial and vaccination. However, armed conflicts can complicate outbreak interventions due to the widespread disruption they cause to the government and the population. Guinea and the Democratic Republic of Congo have historically reported the largest and the most recent Ebola virus outbreaks, and understanding if conflict has played a role in these outbreaks may help in identifying key risks factors which can be used to improve disease control. Methods We used data from a range of publicly available data sources for both Ebola virus cases and conflict events for 2018 to 2021 in Guinea and the DRC. We fitted these data to conditional logistic regression models using the Self-Controlled Case Series methodology, to quantify the magnitude in which conflict increased the risk of reported Ebola virus cases in terms of incidence rate ratio. We re-ran our analysis sub-nationally, by conflict sub-event type and tested the effect of lag. Results Conflict was significantly associated with an increased risk of reported EVD cases in both the DRC and Guinea in recent outbreaks. The effect was of a similar magnitude at 1.88 and 1.98 for the DRC and Guinea, respectively. The greatest effects (often higher than the national values) were found in the most conflict prone areas and during protest/riot-related conflict events. Conflict was influential in terms of Ebola virus risk from 1 week following the event and remained important and, in some cases, more so by 10 weeks. Conclusion Extra vigilance is needed following protests and riot-related conflict events in terms of Ebola virus transmission. These events are highly disruptive in nature, in terms of access to transportation and healthcare and are often in dense urban areas, with high population densities. Additional public health messaging around these types of conflict events, relating to the risks and clinical symptoms may be helpful in reducing transmission. Future work should aim to further understand and quantify conflict severity and intensity, to evaluate a dose-response relationships in terms of disease risk.