The Amazon rainforest covers roughly 40% of Colombia’s territory and has important global ecological functions. For more than 50 years, an internal war in the country has shaped this region. Peace negotiations between the government and the Revolutionary Armed Forces of Colombia (FARC) initiated in 2012 resulted in a progressive de-escalation of violence and a complete ceasefire in 2016. This study explores the role of different deforestation drivers including armed conflict variables, in explaining deforestation for three periods between 2001 and 2015. Iterative regression analyses were carried out for two spatial extents: the entire Colombian Amazon and a subset area which was most affected by deforestation. The results show that conflict variables have positive relationships with deforestation; yet, they are not among the main variables explaining deforestation. Accessibility and biophysical variables explain more variation. Nevertheless, conflict variables show divergent influence on deforestation depending on the period and scale of analysis. Based on these results, we develop deforestation risk maps to inform the design of forest conservation efforts in the post-conflict period.