MnOx deposits in distribution pipes can cause severe discoloration problems in drinking water. However, the impact of pipe materials on Mn(II) oxidation and MnOx accumulation remains unclear. This study investigated microbial-mediated Mn(II) oxidation and deposit formation through 300-day pipe loop experiments with corroded galvanized steel pipes (DN100) and new polyvinyl chloride (PVC) pipes (DN100). The results showed that influent Mn(II) was entirely oxidized within 48 h in the PVC pipes with biofilms in the absence of chlorine, while most influent Mn(II) remained unoxidized in the iron pipes. Dissolved oxygen (DO) monitoring showed that the DO in the PVC pipes was consistently higher than 8.0 mg/L, but that in the iron pipes dropped to 6.5 mg/L. Microbial analysis revealed that the abundance of potential Mn(II)-oxidizing bacteria in the low-DO iron pipes was less than that in the PVC pipes. Analysis of the Mn(II) concentration dynamics in different pipes revealed that the early Mn(II) disappearance in the iron pipes was contributed mainly to Mn(II) adsorption by iron corrosion products rather than microbial Mn(II) oxidation. When aeration was performed to increase the DO concentration to 8.0 mg/L in the iron pipes, complete Mn(II) oxidation occurred. This study provides insights into Mn(II) transformation in different pipes and highlights the critical role of DO in microbial Mn(II) oxidation in drinking water pipes.