Manganese is widely distributed in the natural environment, and its presence in drinking water poses a risk to human health. In this study, an integrated pre-deposited powdered activated carbon (PAC) and manganese oxide (MnOx) bio-functional layer of inorganic origin was coupled with gravity-driven ceramic membrane (GDCM) reactor. The study aims to investigate the effects of the membrane pore size and functional layer integrity on the Mn2+ removal and flux. The results reveal that the average Mn2+ removal efficiency of the large pore size membranes (300 kDa and 0.45 μm) was lower (75 % – 78 %) compared to those with smaller pores (15 kDa and 50 kDa) (87 % – 88 %) during long-term operation. Such differences are attributed to a period of manganese leakage before the PAC-MnOx matured in large-pore membrane units and a longer residence time in small-pore membranes. The functional layer leaded to reversible fouling, which was more prominent in membranes with larger pores (contributing to 93 % of total resistance) than those with smaller ones (ranging from 51.7 % to 61.9 %). Although the damaged functional layer resulted in occasional high Mn2+ concentrations in the effluent, it did not significantly impact long-term flux development. Optical coherence tomography (OCT), in conjunction with COMSOL analysis, non-destructively evaluate biofilm formation process and indicate a homogeneous flow field and mass transfer in the “dual layers” (active film layer and ceramic membrane layer) of the GDCM. The presence of manganese-oxidizing bacteria (Hyphomicrobium, Reyranella, and Pseudomonas) in the GDCM reactor was verified using confocal laser scanning microscopy (CLSM) and high-throughput sequencing. Additional material characterization revealed that a portion of the PAC-MnOx exhibited characteristics of birnessite, with autocatalytic oxidation of Mn2+, and that Mn (III) and Mn (IV) were the primary species in MnOx, which exhibited excellent catalytic oxidation and adsorption capabilities for Mn (II), respectively. Overall, the developed PAC-MnOx GDCM system shows great promise in efficiently removing manganese and producing water of desired quality, thereby holding potential in applications across several sectors of advanced water treatment processes.