Sustainable chemistry concepts are illuminating the path for researchers to utilize tree branches in cellulose industries. 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 morphlogies—ranging from extended fibers to folded sheets, have semi-crystalline structures with appropriate crystalline particle 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. Kinetic study for two pollutants in various concentrations (3, 9 and 12 ppm) showed that the reactions followed the first kinetic model. This study provides a promising future perspective for applying the rich potential of plants in environmental science.