Deforestation is a documented driver of biodiversity loss and ecosystem services in the tropics. However, less is known on how interacting regional and local-level anthropogenic and ecological disturbances such as land use activities, human populations, and armed conflict affect carbon storage and emissions in Neotropical forests. Therefore, we explored how local-scale, socio-ecological drivers affect carbon dynamics across space and time in a region in Colombia characterized by deforestation, land use cover (LULC) changes, and armed conflict. Specifically, using available municipal level data from a period of armed conflict (2009–2012), spatiotemporal analyses, and multivariate models, we analyzed the effects of a suite of socio-ecological drivers (e.g., armed conflict, illicit crops, human population, agriculture, etc.) on deforestation and carbon storage-emission dynamics. We found that about 0.4% of the initial forest cover area was converted to other LULC types, particularly pastures and crops. Gross C storage emissions were 4.14 Mt C, while gross carbon sequestration was 1.43 Mt C; primarily due to forest regeneration. We found that livestock ranching, illegal crop cultivation, and rural population were significant drivers of deforestation and carbon storage changes, while the influential role of armed conflict was less clear. However, temporal dynamics affected the magnitude of LULC effects and deforestation on carbon storage and emissions. The approach and findings can be used to better inform medium to long-term local and regional planning and decision-making related to forest conservation and ecosystem service policies in Neotropical forests experiencing disturbances related to global change and socio-political events like armed conflict.