Against the backdrop of the competing demands of agricultural productivity and biodiversity conservation, understanding land-use changes is critical. We studied the past, current and future landscape dynamic scenarios for coffee and rice-coupled crops at a village scale in the Western Ghats (southern India) by integrating three levels of organization (patch, farm and soils). The village structures and dynamics from 1950 to 2010 were modelled with the Dynamic Patch Landscape (DYPAL) modelling platform and analysed with Comparison Map Profile (CMP) spatial analysis in order to assess environmental trends. Our model, combined with mathematical formalizations and multiscale analyses, was also used to project future land-use sustainability. Our findings highlight significant environmental issues affecting the Western Ghats biodiversity hotspot, which is also subject to increasing and differential demands for other crops that are dependent on farm production systems. Intensive coffee cultivation, with conversion of the forest cover into Grevillea robusta monoculture and ongoing paddy abandonment,have had a strong impact on the region’s landscape (+30% G. robusta) and biodiversity (from –3% to –13% in the already-reduced forest cover).