Conservation and monitoring of tropical forests requires accurate information on their extent and change dynamics. Cloud cover, sensor errors and technical barriers associated with satellite remote sensing data continue to prevent many national and sub-national REDD+ initiatives from developing their reference deforestation and forest degradation emission levels. Here we present a framework for large-scale historical forest cover change analysis using free multispectral satellite imagery in an extremely cloudy tropical forest region. The CLASlite approach provided highly automated mapping of tropical forest cover, deforestation and degradation from Landsat satellite imagery. Critically, the fractional cover of forest photosynthetic vegetation, non-photosynthetic vegetation, and bare substrates calculated by CLASlite provided scene-invariant quantities for forest cover, allowing for systematic mosaicking of incomplete satellite data coverage. A synthesized satellite-based data set of forest cover was thereby created, reducing image incompleteness caused by clouds, shadows or sensor errors. This approach can readily be implemented by single operators with highly constrained budgets. We test this framework on tropical forests of the Colombian Pacific Coast (Chocó) - one of the cloudiest regions on Earth, with successful comparison to the Colombian government's deforestation map and a global deforestation map.