The extraction of rare earth elements (REEs) from phosphogypsum (PG) is of great significance for the effective utilization of rare earth resources and enhancing the resource value of PG waste residues. This study used Aspergillus niger (A. niger) fungal culture filtrate as a leaching agent to investigate the behavior of extracting REEs from PG through direct and indirect contact methods. According to the ICP-MS results, direct leaching at a temperature of 30 °C, shaking speed of 150 rpm, and a solid–liquid ratio of 2:1, achieved an extraction rate of 74% for REEs, with the main elements being yttrium (Y), lanthanum (La), cerium (Ce), and neodymium (Nd). Under the same conditions, the extraction rate of REEs from phosphogypsum using an A. niger culture filtrate was 63.3% higher than that using the simulated organic acid-mixed solution prepared with the main organic acid components in the A. niger leachate. Moreover, the morphological changes observed in A. niger before and after leaching further suggest the direct involvement of A. niger’s metabolic process in the extraction of REEs. When compared to using organic acids, A. niger culture filtrate exhibits higher leaching efficiency for extracting REEs from PG. Additionally, using A. niger culture filtrate is a more environmentally friendly method with the potential for industrial-scale applications than using inorganic acids for the leaching of REEs from PG.

With the rapid development of modern industry, particularly in the fields of electric vehicles and renewable energy technologies, the demand for rare earth elements (REEs) has surged dramatically. Phosphogypsum (PG), which is an industrial waste product generated during the production of phosphoric acid through the sulfuric acid process, is rich in REEs. However, traditional chemical leaching methods pose environmental pollution and resource wastage issues. This study aims to explore the feasibility and optimal conditions for bioleaching REEs from phosphogypsum using Gluconobacter oxydans (G. oxydans). The phase composition and components of phosphogypsum, as well as the growth characteristics and leaching efficiency of G. oxydans, were analyzed in detail using SEM, EDS, XRD, and XRF techniques. Experimental results indicate that G. oxydans can effectively leach REEs from phosphogypsum under conditions of 28 °C, an agitation speed of 150 rpm, and a liquid-to-solid ratio of 4:1, with a maximum leaching efficiency of 24.67%. Moreover, it is revealed in the study that G. oxydans exhibits selectivity in leaching REEs. Specifically, the leaching efficiency for Nd is significantly enhanced at low pH values. This research provides a theoretical basis and practical application example for the efficient and environmentally friendly recovery of REEs from phosphogypsum.