Sustainable chemistry concepts are illuminating the path for researchers to utilize tree branches in the cellulose synthesis, preparation/, or fabrication processes. This represents a revolutionary solution that links waste management with the transition to a green economy, aiming to reduce harmful carbon emissions resulting from burning and replace them with bio-based materials for important environmental remediation. The central objective of this research was to isolate the cellulose-based structure in nano-size from three sources of shrub and tree stems: bougainvillea, fig, and pine, using an alkaline method followed by bleaching with hydrogen peroxide. The nanocellulose samples (N-Cell.bo., N-Cell.fi., N-Cell.pi.) were physicochemically characterized using XRD, FTIR, and FESEM to confirm the isolation of the cellulose phase and the absence of accompanying impurities. Physicochemical characterization revealed that the nanocellulose samples have diverse morphologies—ranging from extended fibers to folded sheets—and have semi-crystalline structures with appropriate crystalline sizes, and are rich in functional groups of sugar units. The ability of the (N-Cell.bo, N-Cell.fi., N-Cell.pi.) samples to remove aflatoxin B1 and Allura Red Ac was studied in both alkaline (pH 8 and10) and acidic media (pH 4 and 6). The removal study demonstrated very good removal efficiency, depending on the type of pollutant and the medium. A kinetic study of two pollutants at various concentrations (3, 9 and 12 ppm) showed that the removal reactions were attribute to a first-order kinetic model. This study provides a promising future perspective for applying the rich potential of plants in environmental science.