Between 2016 and 2021, the area under durian (Durio zibethinus Murr.) cultivation expanded by 29% in Malaysia, with farmers increasingly preferring high-value varieties such as Musang King. During the durian tree’s five-year vegetative stage, intercropping with crops like sweet corn and groundnut offers farmers an additional income stream and supports durian growth. From January 2020 to April 2021, a two-season study at Pusat Pertanian Putra Puchong, Universiti Putra Malaysia, employed a between-subjects design, comparing durian plots with and without intercropping. Crop growth variables and soil physical and chemical properties were measured, and differences were analyzed using independent t-tests. Results showed that intercropping had minimal effects on durian seedling height, canopy diameter, and stem girth. However, the intercropping practices significantly increased chlorophyll a (by 17.80%), chlorophyll b (11.57%), total chlorophyll (15.46%), and carotenoid content (28.57%) in durian leaves. Soil quality also improved in the intercropped plots, with pH rising from 4.35 to 5.38 and calcium concentration increasing from 0.07 to 0.30%, representing 1.89% and 109.46% increases compared to the control plot after the second season. Soil compaction was reduced, as penetration resistance dropped from 1.59 MPa in the control to 0.70–0.78 MPa in the intercropped plots. These findings indicate that intercropping sweet corn and groundnut in young durian orchards can be considered a sustainable practice, enhancing soil health and diversifying farmers’ income without compromising durian growth. Farmers are encouraged to adopt intercropping during the non-fruiting stage to maximize both economic and agronomic benefits.