P-Chloro-Meta-Xylenol (PCMX) is a widely used disinfectant. In the current pandemic scenario, its consumption has increased largely, and as a result, wastewater is loaded heavily with PCMX as a contaminant. Remediation of this ecologically toxic phenolic compound is therefore a burning issue. This study proposes an eco-friendly biosorption-based remediation technique to remove PCMX. A novel isolated phenol-resistant gram-negative bacterium, Pandoraea sp. strain BT102, is first encapsulated in biopolymeric calcium alginate beads. These beads are packed in a long adsorption tube and the contaminated water was passed through this packed tube resembling a plug flow reactor. This unique plug-flow set-up is capable of reducing PCMX concentration from 100 mg L−1 to 2.85 μg L−1 within 4 h using only 30 g of adsorbent, resulting in 99.99% removal efficiency. Adsorption isotherms and kinetics are studied using batch experimental data. A PCMX loading capacity of the encapsulated calcium alginate beads is found to be 961.7 mg g−1, and the Freundlich isotherm results suggested the phenomenon of cooperative adsorption. A good agreement of the pseudo-second-order kinetic model along with the intra-particle diffusion model suggests a multilayer diffusion-controlled adsorption process. Biosorption of PCMX by the bacterium-modified beads was confirmed by Transmission Electron Microscopy (TEM), Scanning Electron Microscopy (SEM), Energy Dispersive X-ray (EDX), and Fourier-Transform Infrared spectroscopy (FT-IR) analyses. The application of multivariate model-based Response Surface Methodology (RSM) reveals flow rate to be the most important factor controlling the rate of bioremediation.