Spent catalysts produced by oil refinery industries are regarded as an important secondary source for valuable metals. In particular, spent fluid catalytic cracking (FCC) catalysts represent a potential source for rare earth elements (REEs). This study aimed to exploit the leachability of spent FCC catalysts as a secondary source for La, by using an alternative organic acid lixiviant produced under optimized fungal fermentation conditions. The first chemical leaching tests revealed that citric acid (>100 mM) is a comparable alternative lixiviant to conventional inorganic acids (1 M) and that the La dissolution behavior changed significantly with different types of organic acids. The initial fungal fermentation conditions (e.g., inoculum level, substrate concentration, pH) largely affected the resultant biogenic acid composition, and its manipulation was possible in order to almost solely ferment citric acid (~130 mM) while controlling the production of unwanted oxalic acid. The performance of actual biogenic acids (direct use of cell-free spent media) and artificially reconstituted biogenic acids (a mixture of chemical reagents) was nearly identical, achieving a final La dissolution of ~74% at a pulp density of 5%. Overall, the microbiological fermentation of organic acids could become a promising approach to supply an efficient and environmentally benign alternative lixiviant for REE scavenging from spent FCC catalyst wastes.