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The north-eastern escarpment of Madagascar harbours the island’s last remaining large-scale humid forest massifs surrounded by a small-scale agricultural mosaic. There is high deforestation, commonly thought to be caused by shifting cultivation practiced by local land users to produce upland rice. However, little is known about the dynamics between forest and shifting cultivation systems at a regional level. Our study presents a first attempt to quantify changes in the extent of forest and different agricultural land cover classes, and to identify the main dynamics of land cover change for two intervals, 1995–2005 and 2005–2011. Over the 16-year study period, the speed of forest loss increased, the total area of upland rice production remained almost stable, and the area of irrigated rice fields slightly increased. While our findings seem to confirm a general trend of land use intensification, deforestation through shifting cultivation is still on the rise. Deforestation mostly affects the small forest fragments interspersed in the agricultural mosaic and is slowly leading to a homogenization of the landscape. These findings have important implications for future interventions to slow forest loss in the region, as the processes of agricultural expansion through shifting cultivation versus intensified land use cannot per se be considered mutually exclusive.