Sporopollenin microcapsules (sporopollenin exine capsule (SEC)) have characteristic holes with 25 μm diameter and can be chemically obtained from the natural pollen grains. In this paper, a BODIPY derivative was successfully immobilized on SEC modified with 3-(aminopropyl)triethoxysilane (APTES) to obtain a fluorescent microcapsule sensor (Sp-APTES-monoBODIPY) and then it was used for both sensitive-selective detection and removal of Cu (II) ions. The prepared surfaces were characterized by several techniques like FT-IR, SEM, XRD. The photophysical measurements (response time, pH, complex stoichiometry, etc.) were fluorometrically performed for the detection of Cu (II) ions in the fluorescence spectroscopy. The limit of detection (LOD) and quantified (LOQ) are 4.9 × 10−7 M and 1.2 × 10−6 M for the detection of Cu (II) which is challenging, respectively. Otherwise, about the removal of Cu (II) with Sp-APTES-monoBODIPY fluorescent microcapsule, we also calculated the maximum isotherm parameters and adsorption capacities from the Freundlich, Dubinin-Radushkevich and Langmuir equations. When the Sp-APTES-monoBODIPY was used as an adsorbent for the removal of Cu (II) ions, the adsorption kinetics and isotherms well fitted the pseudo-second-order model and the Langmuir model, respectively. The maximum adsorption capacity is 25 mg.g−1. All results showed that the synthesized fluorescent microcapsule can be used as an ideal adsorbent and sensor material of Cu (II) ions for simultaneous environmental cleaning applications.