In this study, the efficiency of poly(ethylene glycol dimethacrylate-N-methacryloyl-amido-l-tryptophan methyl ester) [PEDMT] microbeads (in the diameter range of 106–180 µm) as a support material for HRP immobilization was evaluated and the immobilized-HRP enzyme was used for decolorization of Congo Red (CR) and Reactive Black 5 (RB5) dyes. The specific surface area of the PEDMT microbeads was 1103 m2 g−1, which is very high. The PEDMT microbeads had a pore volume and pore size of 1.94 cm3 g−1 and 9.99–55.3 Å, respectively. The chemical compositions of the PEDMT and PEDMT–HRP microbead surfaces were analyzed using X-ray photoelectron spectroscopy (XPS). Immobilization yield, activity yield, and immobilization efficiency were 84.9 ± 2.1, 73.8 ± 5.9%, and 86.9 ± 6.9%, respectively. Optimum pH (6.0), temperature (45 °C and 50 °C for free and immobilized enzyme), H2O2 concentration (3% v/v) were investigated in detail. Thermal and storage stability was increased after immobilization and immobilized enzyme preserved more than 55% of its initial activity even after 10 consecutive uses. Decolorization studies were also performed by investigating the effects of pH, CR, and RB5 concentration, enzyme amount, H2O2 concentration, contact time on decolorization efficiency. The decolorization efficiency for CR and RB5 by PEDMT–HRP was 98.20% and 47.99% after 30 min at pH 6.0 and 45 °C. The immobilized-HRP retained 89% and 27% of its initial activity after three repeated cycles with CR and RB5, respectively. The PEDMT microbeads with high surface area, porosity, durability, and reusability exactly met the requirements for HRP immobilization and dye decolorization.