Borno State, in the northeast of Nigeria, has been reduced from a dynamic and populated rural area into a zone of displacement, hazards and food insecurity due to escalating levels of violence. Since 2009, the conflict has devastated households’ agricultural livelihoods, imposed levies on transportation, and constrained access to market and trade facilities. Agricultural production dramatically reduced due to mass displacement and limited access to markets. Consequently, the food security is alarming with over 1.5 million people estimated to be in food crises, emergency and famine in 2017 that leads to food and nutrition stress and prevalence of diseases such as malaria, cholera and diarrhea due to limited access to water and poor hygiene. In 2018, The Food and Agriculture Organization of the United Nations, United Nations Women and World Food Programme developed a Joint Action Programme aiming to build the resilience of conflict affected population and public sector institutions in Borno State in an environmentally-friendly and sustainable way. The project aims at “Restoring and promoting sustainable agriculture based livelihoods for food security, employment and nutrition improvement in Borno State”. In that respect, this baseline study was conducted to benchmark resilience and food security indicators in the intervention areas. The results show that the household resilience capacity is lower and heterogeneous between the local government areas, and between internal displacement persons, returnee and host households. The internal displacement persons and returnee are the most exposed to food insecurity. The promotion of access to basic services, productive asset, and ad hoc emergency food assistance interventions will increase household resilience and improve food security in Borno State.