The development of high-performance, eco-friendly and magnetic sensors prepared from natural products have recently attracted a lot of attention for the selective detection of metal ions in aqueous environments and the simultaneous detection of metals in the same environment. In this study, a fluorescent and magnetic sensor (MSp-P[5]-EN-B) was prepared by the immobilization of Bodipy and pillar [5]arene on the sporopollenin surface modified by Fe3O4 for the selective detection of Ag+ and Hg2+ ions separately and together in the aqueous solution. The characterization of the fluorescent and magnetic sensor, MSp-P[5]-EN-B, was supported by techniques such as SEM, FT-IR, and XRD. The fluorescence data of MSp-P[5]-EN-B sensor was examined with various concentrations in the range 1–100 μM that in here, an “on-off” fluorescence process for Ag+, and Hg2+ and the detection limits are 0.019 μM and 0.33 μM, respectively. As a result, the designed magnetic MSp-P[5]-EN-B sensor showed strong potential in terms of its accurate, sensitive, and practical application in the separate and simultaneous detection of Ag+ and Hg2+ ions in aqueous media.