Per- and polyfluoroalkyl substances (PFAS) are highly persistent organic pollutants due to their strong C–F bonds, which contribute to their environmental persistence and associated health risks. Naturally-occurring microbes have the ability to degrade PFAS, with Pseudomonas genus showing the highest efficiency, including Pseudomonas plecoglossicida (75%) and Pseudomonas aeruginosa (67%), which has received much attention. This review explores the underlying mechanisms during microbial PFAS degradation, emphasizing bond cleavage processes, including C–F and C–Cl bonds, and the critical roles of microbial enzymes. Microorganisms utilize specialized metabolic strategies to actively cleave chemical bonds within PFAS molecules, initiating their breakdown. Additionally, microorganisms secrete specific enzymes, which play pivotal roles in catalyzing PFAS degradation. Microorganisms and their enzymes can transform and/or defluorinate PFAS through different metabolic processes, improving the efficiency of PFAS degradation. This review further explores the current challenges in PFAS biodegradation and outlines future research directions, aiming to help future studies overcome these obstacles and drive progress in this field.