Following more than 20 years of civil unrest, environmental information for Southern Somalia is scarce while there is clear evidence that the war economy fuelled by the conflict is rapidly depleting the country’s natural resources, 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 early 2011 and early 2013 for developing a semi-automatic mapping method of charcoal production sites as a proxy of tree loss over a 6000 km2 area along the Juba River in Southern Somalia. The user’s accuracy of semi-automatic charcoal production site detection varied between 81.7% for 2011 and 87.3% for 2013, while the producer’s accuracy was 68.2% and 65.5% respectively and, as compared to visual interpretation, reduced significantly the required time. The analysis of the changes between the two dates led to an average tree loss estimation of 3.3%, corresponding to 520,520 trees over the 2 years period. The results help to better understand the dimension and impact of charcoal production in Southern Somalia and are a first step towards the development of a charcoal production monitoring system.