The adoption of agroforestry system aims to combine food production enhancement to compensate population growth with the improvement of agricultural marketable products to increase household income. The diversification of food crop products requires more effective land use. In Gunungkidul, high-density teak (Tectona grandis) plantation has dominated many private forests. The area under the tree crown has received low light intensity, where only shade-resistant plants can survive. Tuber crops, i.e., arrowroot (Maranta arundinacea), canna (Canna edulis) and yam (Dioscorea esculenta) are shade-tolerant crops, which were planted in tree understory for supplementary food production and income generation. The cultivation under teak stand has been overlooked due to uncertainty in tuber productivity. To address this knowledge gap, the effect of teak shade (5- and 7-year teak) on the growth and yield of the three tuber crops was examined. The results indicated that both teak trial areas (with RLI 45.13% and 38.76%) were suitable for canna production (LER > 1), while management options were recommended for enhancing arrowroot and yam production. The LER of intercropped three-tuber crops under 5 years’ teak were >1, while of those under 7 years’ teak, only canna reached >1. Canna is the preferred option to be mixed in teak agroforestry systems with low light intensity due to its consistent yields, whether planted in open area or under teak shade. Silvicultural management, pruning and thinning are recommended to increase the growing space and resource sharing for intercropped plants. Land optimization in private forest understory using shade-resistant tubers will offer medium-term benefits, provided that proper silvicultural procedures are applied.