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Little is known about land cover change in mixed agroforestry systems, which often supply valuable ecological services. The authors use a spatial regression model to analyze clearing in El Salvador’s shade coffee–growing regions during the 1990s. Their findings buttress previous research suggesting the relationship between proximity to cities and clearing in mixed agroforestry systems is the opposite of that in natural forests. But this result, and several others, depends critically on the characteristics of the growing area, particularly the dominant cleared land use. These findings imply that policies aimed at retaining mixed agroforestry need to be carefully targeted and tailored.