We investigated the dynamics and microbial pathways of three up-flow anaerobic sludge bed (UASB) anaerobic ammonium oxidation (anammox) bioreactors using an integrated multichannel sensor system: Reactor 1 (control), Reactor 2 (yarn and hollow-ball matrix), and Reactor 3 (vinylon filament-loaded polyethylene). Electrochemical electrodes, optical spectrophotometers, and thermal digestion sensors were used for continuous monitoring across cellular autolysis (Days 1–12), activity lag (Days 13–22), and activity acceleration (Days 23–132). Sensor data showed that filler matrices enhanced biomass retention and stabilized reactor performance. Under increased nitrogen loading, Reactors 2 and 3 showed a near complete removal of ammonium and nitrite, with efficiencies of 99.88 and 99.99%, respectively. Specific anammox activity increased to 2.17 ± 0.12 mg total nitrogen (TN)/g volatile suspended solids (VSS)/h in Reactor 2 and 2.70 ± 0.44 mg TN/g VSS/h in Reactor 3, representing 72 and 66% growth accelerations. Cytochrome c content increased by 153% in Reactor 3, and extracellular polymeric substances (EPS) increased to 51.12 ± 1.48 mg/g VSS in Reactor 2 and 57.89 ± 2.17 mg/g VSS in Reactor 3, supporting granule maturation. Hydrazine dehydrogenase (HDH) activity peaked at 754.69 ± 58.78 µmol/g protein/min in Reactor 2. The developed sensor system with filler-assisted biomass stabilization enables the nondestructive, high-resolution monitoring of rapid metabolic transitions. To mitigate sensor drift from ion interference and optical biofouling, automated calibration and adaptive sensor design are required. This necessitates filler matrix optimization for sustained granulation and developing self-correcting sensor algorithms.