We describe changes in the cropland distribution for physiographic and bioregions of continental Ecuador between 2000 and 2016 using Landsat satellite data and government statistics. The cloudy conditions in Ecuador are a major constraint to satellite data analysis. We developed a two-stage cloud filtering algorithm to create cloud-free multi-temporal Landsat composites that were used in a Random Forest model to identify cropland. The overall accuracy of the model was 78% for the Coast region, 86% for the Andes, and 98% for the Amazon region. Cropland density was highest in the coastal lowlands and in the Andes between 2500 and 4400 m. During this period, cropland expansion was most pronounced in the Páramo, Chocó Tropical Rainforests, and Western Montane bioregions. There was no cropland expansion detected in the Eastern Foothill forests bioregion. The satellite data analysis further showed a small contraction of cropland (4%) in the Coast physiographic region, and cropland expansion in the Andes region (15%), especially above 3500m, and in the Amazon region (57%) between 2000 and 2016. The government data showed a similar contraction for the Coast (7%) but, in contrast with the satellite data, they showed a large agricultural contraction in the Andes (39%) and Amazon (50%). While the satellite data may be better at estimating relative change (trends), the government data may provide more accurate absolute numbers in some regions, especially the Amazon because separating pasture and tree crops from forest with satellite data is challenging. These discrepancies illustrate the need for careful evaluation and comparison of data from different sources when analyzing land use change.