Shade trees stimulate many pathways that influence disease development in opposite directions, and that, in addition, may interact with environment. To better understand shade trees effects on coffee leaf rust (CLR), we studied three disease stages separately: sporulation, uredospore wash-off by rain, and uredospore deposition on leaves. The study was conducted during almost one year in the long-term trial on coffee-based agroforestry systems established by CATIE in 2000, in Turrialba, a low altitude area of Costa Rica. We only used the Full Sun and Shade provided by Chloroleucon eurycyclum treatments. For studying sporulation, we harvested diseased leaves every three weeks and collected the uredospores present on the lesions. For assessments of uredospore wash-off, we located containers at ground level below the coffee bushes and in the interval between rows of coffee bushes, and removed them after rainfall events (43 rainfall events studied) to count the number of uredospores collected. For uredospore deposition, we used varnish to capture deposited uredospores on apparently healthy coffee bush leaves (55 dates). We also studied the raindrop kinetic energy by using splashcups, on 19 rainy days. The number of uredospores produced and preserved was 2.22 times higher below shade trees than in full sun, whereas the number of uredospores lost by wash-off, below the coffee bush, was 1.62 times lower. Reduced wash-off was probably due to raindrop interception by shade trees and stemflow and to the increased kinetic energy of the raindrops in the understory of the Shade treatment (twice as high as that measured in full sun), which reduced the capacity of coffee leaves to intercept raindrops. In addition, we found 1.43 times more uredospores deposited on apparently healthy leaves below shade trees than in full sun, partly due to the higher number of uredospores produced and preserved below shade trees. Increasing throughfall and reducing raindrop kinetic energy below shade trees seem crucial to improved CLR regulation. This can be achieved by selecting specific shade tree functional traits and by implementing shade pruning during the rainy season.