Nitrate contamination in groundwater is a global concern due to its widespread presence and consequential social, environmental, and economic ramifications. This study investigates the efficacy of biological denitrification in a humid tropical setting, utilizing corn cob in batch and column tests to assess nitrate removal under varying conditions. Batch tests demonstrated the nitrate removal efficiencies of 93.14%, 91.58%, 90.77%, and 98.74% for initial concentrations of 22.18 ± 2.82 mg/L, 27.3 mg/L, 69.1 ± 1.2 mg/L and 115.08 ± 1.88 mg/L, respectively. In the column test, the removal efficiency was 99.86%, 87.13%, and 74%, and the denitrification rate was 32.82, 53.43, and 83.53 mg NO3−-N/L d, for a hydraulic retention time (HRT) of 24 h, 16 h, and 7 h, respectively. Predominantly, nitrate removal occurred via biological denitrification, particularly favoring a 24 h HRT. The corn cob effectively removed high nitrate concentrations of up to 115 mg NO3−-N/L. Scanning electron microscopy and Fourier transform infrared spectroscopy revealed surface characteristic changes of the carbon source pre- and post-denitrification. This research sheds light on the potential of biological denitrification using corn cob in humid tropical environments, offering a promising avenue for addressing nitrate contamination challenges in groundwater systems.