Shade trees may have contrastive effects on Robusta coffee (Coffea canephora Pierre ex A. Froehner) yield, which may be additionally influenced by soil properties and reproductive stages of the plant. The current study is aimed at examining the interaction effects of shade trees, soils with different properties, and reproductive stages on coffee yield and identifying key factors influencing the yield. The current study was conducted in Dakha, Kontum of Vietnam on 133 farms, randomly selected from two soils, and two reproductive stages of coffee plants planted with and without shade trees. The coffee yield was measured, and surface soil samples were taken from these farms to be analyzed for 16 variables. The results showed that shade trees enhanced coffee yield significantly (by 28%) in the young reproductive stage but exhibited an insignificant effect in the old stage. The silt fraction, total nitrogen, cation exchange capacity, and shade trees were key factors determining 52% of the coffee yield in the sandy clay loam soil, while silt content and shade trees determined 23% of the yield in the clay soil. These findings suggest that shade trees, together with some soil properties, should be considered to improve coffee production under a tropical monsoon climate region.