This review evaluates fungal bioreactors for the removal of emerging organic pollutants, focusing on pellet-based and immobilized configurations under different operating conditions. A dataset of 71 studies was analyzed by considering reactor configuration, operating mode, and key operating parameters (e.g., pollutant family, carrier type, and wastewater sterility). Overall, removal efficiency was strongly pollutant-dependent. Exploratory comparisons across the available studies suggested that immobilized systems may perform favorably under continuous operation for selected pollutant families, especially non-steroidal anti-inflammatory drugs and antiepileptics. In the dataset analyzed, these families showed median removal efficiencies of 99% and 74%, in immobilized systems, respectively, compared with 85.5% and 50% in pellet-based systems. These trends may be related to improved biomass retention, reduced washout, and greater operational stability; however, the heterogeneity and non-independence of the available data should be considered when interpreting these comparisons. Carrier effects were context-dependent and were most evident for pesticides, while wastewater sterility mainly influenced continuous immobilized systems by affecting biomass stability, microbial competition, and fungal activity. A major limitation in current studies is the focus on parent compound removal, with a limited assessment of the possible toxicity of transformation products. Future research should prioritize long-term continuous operation under non-sterile wastewater conditions, improved immobilization strategies, carrier durability, and transformation product monitoring.