This study investigated a new approach for synthesizing Bacillus subtilis biofilm-supported Mn–Ce/zeolite catalysts for the degradation of gaseous toluene. Four different metal oxide nano-catalysts (ZMn, ZMnCe-10%, ZMnCe-20%, and ZMnCe-30%) were synthesized with varying ratios of manganese (Mn) and cerium (Ce) on zeolite nanoparticles. TEM, SEM, XRD, BET, XPS, and EDX mapping were used to examine these four samples, as well as simple zeolite. Based on these analyses, the catalytic activity of the prepared samples ZMn, ZMnCe-10%, ZMnCe-20%, and ZMnCe-30% for the complete oxidation of toluene and toluene intermediate products were tested with Non-thermal plasma (NTP) technology in a dielectric barrier discharge (DBD) reactor. Among all, ZMnCe-20% showed the highest toluene degradation efficiency (89%) at low concentrations (200 ppm) and humidity (>50%). Later, highly efficient and hydrophobic nano-biocatalysts were prepared by combining B. subtilis biofilm wild-type (WT) and engineered B. subtilis biofilm EPS with ZMnCe-20% catalyst. EPS is the main component found in biofilm matrix and plays a key role in influencing properties such as biofilm stability, electron transfer, surface roughness and hydrophobicity. Compared to WT B. subtilis biofilm, EPS overexpressed B. subtilis biofilm showed stronger growth and development on ZMnCe-20% nanocatalyst. Moreover, the NTP system packed with ZMnCe-20%/biofilm (EPS+) nano-biocatalyst exhibited the highest toluene degradation activity (99%) with (83%) CO2 selectivity, (up to 50%) reduction in NOx concentration and complete ozone decomposition at (250 ppm) toluene concentrations and increased humidity (>90%). High-energy electrons generated in the NTP system break the C–H and C–C bond between the rings of the toluene molecule, forming several byproducts which are later reacted with active radical species such as O, OH, and O3 and further converted into final degradation products (CO2 and H2O). The results demonstrated successful biofilm development and growth on the ZMnCe-20% catalyst with advanced features such as superhydrophobicity, H2O resistance, improved surface roughness, and electron generation. In short, the study's approach combines bioengineering and material science to develop sustainable nano-biocatalysts for removing VOCs in industrial and environmental settings.