The increasing demand for wood, fiber, and pulp, coupled with efforts to mitigate greenhouse gas emissions, has placed immense importance on the development of forest plantations. The rapidly growing human population faces shortages of food, particularly in the developing world where agricultural productivity is generally low. The taungya system, an age-old agroforestry practice involving the intercropping of crops with trees on the same unit of land, is opined as a win-win strategy to meet the need for wood products and food at the same time. In recent years, the taungya system has gained increasing attention from large forest companies as a tool and an opportunity to contribute to the social well-being of the local community. However, the effects of intercropping on the tree component are largely unexplored. Thus, this study was conducted to examine whether intercropping after 2 and 7 years has an effect on the root system of trees, thereby generating knowledge that supports evidence-based plantation management decisions involving the taungya system. To characterize the root system architecture, trenches were made on six young trees in both a pure Eucalyptus camaldulensis monoculture and intercropped stands (1111 trees/ha in both stands). To quantitatively estimate root biomass, a total of 324 soil cores (6 stands × 6 trees × 3 distances × 3 soil depths) were collected, and roots were sorted and dried to constant mass in an oven at 60 °C for 48 h. The root dry mass data were subjected to analysis of variance to examine the significant effects of intercropping, spacing, and stand age. The results show that the root system of E. camaldulensis was mainly confined to shallow depth but well elongated horizontally in both pure and intercropped stands with 4–6 thick lateral roots. The intercropping of rice/cassava with eucalypt had no effect on the total root dry mass of the tree component (p > 0.05) irrespective of the plantation spacing (5 m × 2 m or 9 m × 1 m); however, root biomass decreased with increasing horizontal distance from the tree base and in deeper soil layers, particularly for trees in young stands. The effects of spacing between trees, wide (5 m × 2 m) versus narrow (9 m × 1 m), on root dry mass were dependent on the horizontal and vertical distribution of the root system, and root biomass appeared to be higher at 40 cm soil depth for the stand with wide spacing between trees than for stands with narrow spacing. Root biomass was larger for older rather than younger trees in both monoculture and intercropped stands, suggesting the lack of a carry-over effect of intercropping on root biomass. In conclusion, this study provides evidence in support of intercropping as a win-win strategy to meet the short-term needs of food production while producing wood in the end. As root biomass varies with horizontal distribution, further research is recommended to test buffer zones between trees and crops other than 1m, which is currently used.