Sporopollenin is a natural substance found in plant walls and is highly resistant to external factors. In this paper, we designed an eco-friendly hybrid material, Sp-EDA-BODIPY, based on sporopollenin microcapsule and BODIPY to remove and detect metal ions. The fluorescent surface was fully characterized with various methods such as XRD, SEM, FT-IR, fluorescence spectroscopy. The fluorescent microcapsule sensor showed fluorometrically a remarkable quenching effect in the presence of Cu (II) ion, via the complexation mechanism that LOD it was calculated as 0.773 μM. As a result of the competing ion experiments, Sp-EDA-BODIPY also has a high selective for Cu (II) ion toward another the studied metal ions. Otherwise, we also calculated the adsorption capacities and the maximum isotherm parameters and from the Freundlich, Langmuir, and Dubinin-Radushkevich equations for the removal of Cu (II) with Sp-EDA-BODIPY fluorescent microcapsule. The maximum adsorption capacities of Cu (II) on Sp-EDA-BODIPY were calculated to be 28.65, 31.25, 34.02, and 37.74 mg/g at different temperatures (298, 308, 318, and 328 K), respectively. The adsorption experimental results were closer to Langmuir adsorption isotherm and pseudo-second-order models. Thermodynamic data showed that the adsorption process was endothermic, possible, and spontaneous.