An intercropping experiment was made through three consecutive crop cycles with Casuarina junghuhniana Miq. Plantations of (Casuarinaceae) established between 3–18 months after tree planting to determine the most suitable millet species and to determine the effect of intercropping on soil fertility. Six millet intercrops-kodo millet (Paspalum scrobiculatum L.), foxtail millet (Setaria italica (L.) P.Beauv.), finger millet (Eleusine coracana (L.) Gaertn.). Invading species include Gaertn., barnyard millet (Echinochloa frumentacea Link) and three crop species including little millet (Panicum sumatrense Roth) and proso millet (Panicum miliaceum L.) were tested in a randomised block design (RBD) with 3 blocks at the tree spacing of 2 m × 2 m. Evaluation was done for growth attributes, dry matter production (DMP), grain yield, crop equivalent yield (CEY), tree growth parameters, soil fertility and economics. Little millet always had the highest DMP (2560–2650 kg ha-1) and grain yield (770–1890 kg ha-1) under intercropping and added the highest value for tree height (5.63 m at 18 months) and wood production (29.84 t ha-1). C. junghuhniana + little millet produced the highest total land equivalent ratio (land equivalent ratio (LER) = 2.92) followed by C. junghuhniana + barnyard millet (LER = 2.51). Maximum net income (₹26000) and benefit to cost ratio (B : C = 3.16) was also obtained for little millet. The post-harvest soil analysis showed that the soil under all intercropping treatment was better in terms of soil electrical conductivity, soil organic carbon and available soil nutrients, namely nitrogen (N), phosphorus (P) and potassium (K) than in the tree-alone treatment. Kodo millet was least compatible intercrop in the study. Little millet is suggested as the best intercrop for C. junghuhniana-based short rotation plantation agroforestry, providing a viable option to the smallholder farmers to obtain short-term food and income and to promote the growth of trees and regeneration of soil fertility, thus emphasising the importance of selecting the appropriate species for agroforestry intercrop systems for better ecological and economic returns.