Acid mine drainage (AMD) remediation facilities can produce treatment byproducts with near ore grade concentrations of rare-earth elements (REEs), cobalt, and manganese. High concentrations of these critical metals in treatment solids are often associated with hydrous manganese oxides (HMOs) through adsorption and/or coprecipitation. Chemical and microbial oxidation processes can influence HMO formation, mineralogy, and sorption efficiency. Here, we investigate the adsorption of rare-earth elements and yttrium (REY), cobalt, and nickel over 31 days by (1) abiotic HMO (δ-MnO2 and c-disordered H+ birnessite) produced by chemical oxidation and (2) bitotic HMO produced by Mn-oxidizing fungi, Paraphaeosphaeria sporulosa and Stagonospora sp. After 31 days, ∼70% of REY was adsorbed by abiotic HMO, whereas >99% of REY was adsorbed by biotic HMO and/or fungal biomass within 7 days. Biotic HMO also adsorbed ∼30% Ni and ∼75% Co; however, Co and Ni adsorption by abiotic HMO was negligible. Both biotic and abiotic HMOs were initially poorly crystalline. However, over the course of the experiment, abiotic HMO was transformed to more crystalline phases, resulting in a reduced adsorption capacity and significant desorption of Co and Ni. In contrast, the biotic HMO remained stable and resistant to structural changes over time. This study demonstrates that biotic HMOs are highly efficient at adsorbing Co and REY and that fungal biomass can also play a significant role in this process, particularly for REY.