Abstract: Indigenous microbial communities were employed after subculture in stirred and column bioleaching experiments involving ion-adsorption type rare earth ore. The microbial eukaryotic communities exhibited dramatically varying diversity and structure across culture compositions. Compared with Czapek and sucrose medium, the community cultured in a nutrient broth (NB) medium had a higher diversity, and it was mainly composed of Zygosaccharomyces, Ustilago, Kodamaea, Malassezia, and Aspergillus. These microorganisms secrete organic acids, such as citric acid, malic acid, gluconic acid, and itaconic acid, which provide effective coordination electrons through hydroxyl and carboxyl groups. Stirred bioleaching experiments were conducted to investigate the effect of community, inoculum dosage, liquid–solid ratio, and time on the leaching efficiency. Stirred bioleaching resulted in a concentration limitation phenomenon. When the inoculum dosage of the community cultured in NB medium was 70vol%, the liquid–solid ratio was 5.0 mL·g⁻¹, and the time was 60 min, the upward trend of rare earths leaching rate has become very small. Specifically, the leaching rates of detectable La, Ce, and Y were approximately 92.49%, 92.42%, and 94.39%, respectively. The leaching efficiency and the three influencing factors all conformed to the Poly5 polynomial function, with variances above 0.99. Column bioleaching experiments were performed at a scale of 1 kg. The self-propelled low-pH environment increased the leaching efficiency, which resulted in a leaching rate of 98.88% for rare earths after 117 h. X-ray diffraction and scanning electron microscopy revealed that the samples mainly comprised quartz, kaolinite, orthoclase, muscovite, and zeolite, which were predominantly present in the form of lumps, flakes, rods, and small particles. After bioleaching, the wave intensity of quartz, kaolinite, orthoclase, and muscovite increased, and that of zeolite decreased considerably. A diminution in the number of fine particles indicated the dissolution of small quantities of clay minerals. Ultimately, the differentiated bioleaching mechanism of various forms of rare earths was discussed based on experimental phenomena.