This study evaluated the performance of biofilm reactors inoculated with azo dye degrading Shewanella for the decolorization of Reactive Black 5 (RB5), using three different carrier materials, namely almond shell biochar, moving bed biofilm reactor (MBBR), and polypropylene carrier (PPC). The reactors were fed with low-nutrient artificial wastewater containing RB5 for a long term, and all three carriers showed good RB5 decolorization performance, with varying efficiencies. LC-MS analysis revealed significant differences in the degradation pathways of RB5 among the carriers, indicating the role of carrier materials and microbial communities. The MBBR carrier exhibited good stability due to its rough surface and microbial aggregates. Sequencing results revealed significant differences in the microbial community structure among the carriers. Shewanella was the dominant functional bacteria in the MBBR and PPC carriers, while highly efficient degrading microbial communities were observed on the biochar carrier. Overall, the physicochemical properties of the carrier materials had a significant impact on the microbial community in the reactor, which affected the degradation efficiency of RB5. These findings provide valuable insights into the optimization of biofilm reactors for dye-containing wastewater treatment.