The trend of soil degradation in intensive open coffee systems is well-documented. This study highlights the impact of young shade trees on soil quality only 4 years after their intercropping with coffee. 18 young shade trees belonging to three tree species (Cinnamomum camphora, Bishofia javanica and Jacaranda mimosifolia) were selected in an intensive coffee system in Southern Yunnan. Soil samples (0–20 cm) were tested for chemical composition, soil communities and soil enzyme activities under their canopies and in open areas, both in coffee rows and inter-rows, once during the rainy and once during the dry season. Additionally, root systems were characterized using trenches. Soil water profiles and litterfall were monitored along the production cycle. Coffee yield was recorded for two consecutive years. We detected a positive impact of all shade tree species on soil chemical, biological and biochemical components, especially during the dry season. This positive impact included higher soil organic matter (+10%) and more abundant soil microbial communities (+64%) under shaded coffee than under open coffee. Furthermore, shaded coffee trees yielded as much as open coffee trees, except under C. camphora, probably due to high below-ground competition. These results demonstrate that carefully selected shade trees can rapidly contribute to preserving and/or restoring soil quality in intensive coffee systems, while maintaining high coffee yield.