Bioleaching exhibits high potential for the processing of low-grade complex mineral resources. With the development of the economy and an increase in demand, rare earth elements (REEs) in secondary resources, such as phosphogypsum, red mud and coal-related resources, are gaining more and more attention. In this review, the bioleaching performance of diverse microorganisms is summarized and compared for primary (mainly monazite) and secondary REE resources, based on publications from the past decade. The mineral characteristics of these REE resources are different, as they can be found in phosphate, sulfate, or silicate forms. Correspondingly, microbial species suitable for use in bioleaching differ. The most efficient bioleaching microbe for monazite is Paecilomyces sp., while Acidianus manzaensis is effective in processing red mud. Acidophilic sulfur oxidizers are suitable for processing acidic phosphogypsum. Acidithiobacillus thiooxidans could recover a significant amount of REEs from coal fly ash. In particular, monazite has a high REE content but extremely low bioleaching efficiency compared to that of secondary resources, supporting the understanding that bioleaching approaches are more competitive for minerals with low REE contents. Overall, great progress has been made over the last decade, as considerable REE recovery rates have been achieved, and the main metabolites of microbes were identified. However, numerous challenges still exist. Future efforts should focus on improving biorecovery efficiency, reducing the cost of cell-culture media, and exploring the interaction mechanism between cells and minerals, with an emphasis on mineralogical phase transformations and the molecular regulation mechanisms inside cells during the bioleaching process.