The present work was conducted to evaluate the bioleaching feasibility of red mud with Penicillium chrysogenum strain KBS3 in the presence of glucose, sawdust, and molasses as a substrate and in various leaching modes. The one-step bioleaching system involved 12 mM citric acid, 2.5 mM oxalic acid, 1.8 mM tartaric acid, and 1162 mM gluconic acid, with glucose as the substrate. The biogenic acid production in the two-step bioleaching system involved 15 mM, 1 mM, 0.5 mM, and 152 mM, respectively, and in the spent-medium bioleaching system, it was 63 mM, 29 mM, 23 mM, and 3 mM, respectively, using glucose as the substrate and a pulp density of 3%. The concomitant bio-mobilization of rare earths investigated under different modes were observed to be: 79% Y, 28% La, and 28% Ce in one-step (mode 1) bioleaching; 63% Y, and 28% both La and Ce in the spent-medium (mode 2) bioleaching; and 67% Y, 20% La, and 15% Ce in a two-step (mode 3) bioleaching. On the other hand, the bio-mobilization of rare eaths with molasses as the substrate was found to be: 57% Y, 13.5% La, and 12.7% Ce in mode 4 bioleaching; 57% Y, 14% La, and 12% Ce in mode 5 bioleaching; and 49% Y, 6.3% La, and 2.9% Ce in mode 6 bioleaching of the red mud. Insignificant results were observed using sawdust as the substrate.