Coffee cultivation under agroforestry systems is one of the main agricultural activities in Central America, but climate change is putting its sustainability at risk. Rainfall erosivity has worsened, thus driving soil losses. Although the vegetal covers in coffee agroforestry systems play a crucial role in controlling erosion, the specific influence of each cover layer remains unclear. In this study, we assessed the influence of the canopy (tree and banana cover and coffee cover) and ground cover (weed and litter) on water driven soil erosion, to determine which type of cover has the most influence on soil erosion control. The study site is situated in the core and buffer zones of the Macizo de Peñas Blancas National Park (Nicaragua), where seventeen coffee sampling plots with an agroforestry system composed of an Inga spp and Musa spp canopy cover were analysed. The results showed that the 19.2 ± 3.4% of the soil surface was affected by erosion and it was mainly related to the litter ground cover (r = –0.95, P < 0.001). Also, this cover presented the best partial correlation (ryl.tcw = –0.93, P < 0.001) when the effects of the other vegetal covers were eliminated. Specifically, the litter cover accounted for 90% of the erosion variability, while the impact of the other types of cover was negligible, accounting for just 1% of the erosion. We conclude that litter layer is more important than canopy cover for effective erosion control, and the main function of shade trees is as a source of litter biomass.