Microporous membranes such as polytetrafluoroethylene (PTFE) and polyvinylidene fluoride (PVDF) often exhibit suboptimal hydrophilicity and microbial adhesion, which impede effective nitrogen removal in membrane-aerated biofilm reactors (MABRs), particularly during initial operational phases. To address this issue, the present study introduced acrylic acid (AA) following plasma treatment (P) to enhance membrane performance, thereby engineering a novel composite material optimized for MABR applications. Four MABRs—Reactor with pristine PVDF membrane (R-PVDF), Reactor with composite PVDF membrane (R-PVDF-P-AA), Reactor with pristine PTFE membrane (R-PTFE), and Reactor with composite PTFE membrane (R-PTFE-P-AA)—were evaluated. The modified membranes displayed enhanced roughness and hydrophilicity, which improved biocompatibility and variably increased the oxygen transfer efficiency. Notably, the R-PVDF-P-AA configuration showed a significant enhancement in the removal rates of NH4+-N and total nitrogen (TN), achieving 78.5% and 61.3%, respectively, which was markedly higher than those observed with the original membranes. In contrast, the modified R-PTFE-P-AA exhibited lower removal efficiencies, with NH4+-N and TN reductions of approximately 60.0% and 49.5%. Detailed microbial community analysis revealed that the R-PVDF-P-AA membrane supported robust commensalism between ammonia-oxidizing and denitrifying bacteria, underpinning the improved performance. These findings highlight the critical role of surface chemistry and microbial ecology in optimizing the function of MABRs.