Currently, there is no precise information on the degree of transformation of Tropical Andes hotspot landscape and native ecosystems due to the intensification of agricultural and urban land-use. Proper knowledge of these changes would provide crucial information for planning conservation strategies. We evaluated the impact of the intensification of agricultural and urban land-use on the Inter-Andean Dry Forest and Tropical Montane Forest, both of which are categorized as Critically Endangered, and the state of the landscape in the High Rio Guayllabamba watershed, Ecuador, during the periods 1991–2005 and 2005–2017. The evaluation was carried out using Landsat satellite images of 30 x 30 m pixels and landscape metrics. We found an advanced state of landscape transformation. Since the 1990s, the loss of both ecosystems was largely caused by the conversion of forest to agriculture, resulting in substantial changes in the spatial configuration of these ecosystems. From 1991 to 2017, 19.8 % and 16.1 % of Inter-Andean Dry Forest and Tropical Montane Forest respectively, were converted to agriculture. The loss of Inter-Andean Dry Forest was 28 % and the number of forest patches increased by more than 150%. The loss of Tropical Montane Forest was 16.5 % and the number of forest patches increased by more than 300 %. The largest loss and fragmentation of forest cover occurred from 1991 to 2005. We suggested planning landscape-scale conservation, using the patch-corridor-matrix model. This model is appropriate given the current configuration of the landscape studied, with Inter-Andean Dry Forest and Tropical Montane Forest restricted to small patches sparsely distributed across the landscape.