Water contamination resulting from the presence of organic dye pollutants in the ecosystem is a significant issue in the 21st century, that requires urgent resolution. Utilizing an effective nanocatalyst for the removal of dyes from water is a viable solution to address this problem. In this study, we proposed two distinct approaches for synthesizing δ-MnO2 nanostructures: an environmentally friendly, “green” method (MG) and a “cost-effective” hydrothermal method (MH). The leaf extract of Clinacanthus nutans was used for the preparation of MG, while MnSO4 was used for MH as a reducing agent, along with KMnO4, with the reaction time fixed at 90 °C. X-ray diffraction analysis confirmed that both approaches yielded δ-MnO2 nanostructures with a monoclinic Birnessite phase. The MG sample displayed a coagulated nanoflake-like morphology, as observed in FESEM images. On the other hand, the MH sample exhibited a distinct nanoflower morphology. The materials' optical properties were investigated using UV–visible spectra analysis, revealing direct bandgap energies of 2.2 eV and 2.58 eV for the MG and MH, respectively. The surface area of the MG sample was found to be higher as compared to the MH nanoflower, showcasing a mesoporous structure. XPS analysis was employed to determine the oxidation states of the elements. The effect of varying pH levels on the degradation of Methyl Orange dye by the two nanocatalysts was investigated. The results demonstrated that acidic pH led to higher decolouration efficiency, particularly notable for the MG nanocatalyst. Consequently, this study illustrates that the green δ-MnO2 nanocatalyst effectively degrades methyl orange dye under acidic conditions through photocatalysis.