The recognition of cellulose nanofibrils (CNF) in the past years as a high prospect material has been prominent, but the impractical cellulose extraction method from biomass remained as a technological barrier for industrial practice. In this study, the telescopic approach on the fractionation of lignin and cellulose was performed by organosolv extraction and catalytic oxidation from oil palm empty fruit bunch fibers. The integration of these techniques managed to synthesize CNF in a short time. Aside from the size, the zeta potential of CNF was measured at −41.9 mV, which allow higher stability of the cellulose in water suspension. The stability of CNF facilitated a better dispersion of Fe(0) nanoparticles with the average diameter size of 52.3–73.24 nm through the formulation of CNF/Fe(0). The total uptake capacity of CNF towards 5-fluorouracil was calculated at 0.123 mg/g. While the synergistic reactions of adsorption-oxidation were significantly improved the removal efficacy three to four times greater even at a high concentration of 5-fluorouracil. Alternatively, the sludge generation after the oxidation reaction was completely managed by the encapsulation of Fe(0) nanoparticles in regenerated cellulose.