Removal of Mn(II) from Fe(II)- and Mn(II)-rich groundwater in cold regions is challenging, due to slow Mn(II) removal kinetics below 15 °C. This study demonstrated onset, acclimation, and acceleration of Mn(II) removal in a two-stage pilot-scale biofilter (Fe and Mn filters) at varying low on-site temperatures (8–14.8 °C). Mn(II) removal commenced at 8 °C in the Mn filter after Fe(II) removal. A shift in redox-pH conditions favored biological Mn(II) removal and Mn(II)-oxidizing bacteria increased. The Mn filter reached steady-state functioning after 97 days, exhibiting high removal efficiencies (97 ± 0.9%). Yet, first-order rate constants (k) for Mn(II) removal were low (10−6–10−5 min−1; t1/2 = ∼40 d). After consecutive backwashes and filter inoculation with backwashed sludge, k remarkably accelerated to 0.21 min−1 (t1/2 = 3.31 min at 11 ± 0.6 °C). The cold-adapted microbial consortium (51 genera), including Pseudomonas, Leptothrix, Flavobacterium, and Zoogloea, cultured from the field-aged biofilter rapidly produced biogenic Mn oxides at 8 °C, confirmed by electron paramagnetic resonance spectroscopy. Birnessite and pyrolusite detected by synchrotron-based powder X-ray diffraction, and a repetitive birnessite-like surface morphology on ripened filter materials, reflected autocatalytic oxidation. Shifting in k indicated the vertical progress of biofilter ripening, which was not limited by low temperature.