Following more than 20 years of civil unrest, environmental information for Southern Somalia is scarce while there is clear evidence that the war economy fueled by the conflict is rapidly depleting the country’s natural resources and especially the woody biomass. Wood charcoal production is one of the most relevant businesses supporting war regimes such as the extreme Islamist group Al Shabaab, which has ruled in Southern Somalia from 2006 to 2012 and is still occupying large areas. In this study we first used Very High Resolution (VHR) satellite imagery of February 2013 for developing a semi-automatic mapping method of charcoal production sites as a proxy of tree loss over a 754 km2 woody area along the Juba river in Southern Somalia. The accuracy of semiautomatic charcoal production site detection varied between 80 and 95% as compared to visual interpretation and reduced significantly the subjectivity and the required time. The analysis was then applied to previous years (2011-2012) for a 52.6 km2 subset of the study area, and led to a tree loss estimation of 8.63%, corresponding to 15,434 trees over the 3 years period. The results are crucial for better understanding the dimension and impact of charcoal production in Southern Somalia and are a first step towards the development of a charcoal production monitoring system.