Volatile organic compounds (VOCs) are highly volatile in nature and cause significant air pollution in the environment. It is copiously present in evaporate condensate wastewater (ECWW) released by the pharmaceutical industry and can escape into the atmosphere during conventional aerobic wastewater treatment. This study describes the preparation of molybdenum impregnated nanoporous carbon silica matrix (MoNCSM) and its efficiency toward catalytic oxidation of VOCs present in ECWW. It also focuses on the oxidation of the non-VOCs present in ECWW after VOCs removal. The MoNCSM was characterised by Fourier transform infrared spectroscopy, which confirmed the sharp peaks in the region 800–600 cm−1 corresponding to the stretching vibrations of Mo-O-Mo. The X-ray diffraction spectrum of MoNCSM showed 2θ values of 26.38°, 57°, 31.2° for MoO2, and 40.06° for MoO3. The electron paramagnetic resonance spectrum showed the presence of free electrons in MoNCSM at a g-factor of 2.011. The ECWW possessed chemical oxygen demand (COD) of 210,000–240,000 mg L−1, in which 90–92% account for VOCs. The VOCs were separated from ECWW and catalytically oxidised using MoNCSM catalyst. It showed a removal efficiency of 84.8% ± 2.3 in terms of total organic carbon (TOC) in 20 treatment cycles. The remaining non-VOCs containing ECWW were treated by advanced oxidation processes using sequential packed-bed and fluidised bed reactors. Its overall removal efficiency was COD, 98.78%; biochemical oxygen demand, 98.54%; TOC, 99.46%; total Kjeldahl nitrogen, 78.2%, and NH4+-N, 95%, respectively. The catalytic oxidation of VOCs present in ECWW was confirmed using TOC analysis and high-performance liquid chromatography.