Spent lithium-ion batteries (LIBs) are increasingly generated due to their widespread use for various energy-related applications. Spent LIBs contain several valuable metals including cobalt (Co) and lithium (Li) whose supply cannot be sustained in the long-term in view of their increased demand. To avoid environmental pollution and recover valuable metals, recycling of spent LIBs is widely explored using different methods. Bioleaching (biohydrometallurgy), an environmentally benign process, is receiving increased attention in recent years since it utilizes suitable microorganisms for selective leaching of Co and Li from spent LIBs and is cost-effective. A comprehensive and critical analysis of recent studies on the performance of various microbial agents for the extraction of Co and Li from the solid matrix of spent LIBs would help for development of novel and practical strategies for effective extraction of precious metals from spent LIBs. Specifically, this review focuses on the current advancements in the application of microbial agents namely bacteria (e.g.,Acidithiobacillus ferrooxidansandAcidithiobacillus thiooxidans) and fungi (e.g.,Aspergillus niger) for the recovery of Co and Li from spent LIBs. Both bacterial and fungal leaching are effective for metal dissolution from spent LIBs. Among the two valuable metals, the dissolution rate of Li is higher than Co. The key metabolites which drive the bacterial leaching include sulfuric acid, while citric acid, gluconic acid and oxalic acid are the dominant metabolites in fungal leaching. The bioleaching performance depends on both biotic (microbial agents) and abiotic factors (pH, pulp density, dissolved oxygen level and temperature). The major biochemical mechanisms which contribute to metal dissolution include acidolysis, redoxolysis and complexolysis. In most cases, the shrinking core model is suitable to describe the bioleaching kinetics. Biological-based methods (e.g., bioprecipitation) can be applied for metal recovery from the bioleaching solution. There are several potential operational challenges and knowledge gaps which should be addressed in future studies to scale-up the bioleaching process. Overall, this review is of importance from the perspective of development of highly efficient and sustainable bioleaching processes for optimum resource recovery of Co and Li from spent LIBs, and conservation of natural resources to achieve circular economy.