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In the present study, a natural-based heterogeneous catalyst is synthesized. For this purpose, nano-hydroxyapatite (n-HA) is prepared, silica-modified and functionalized with phthalimide. Finally, Ag2+ was immobilized onto n-HA/Si-PA-SC and reduced to Ag nanoparticles by Bellis perennis flowers extract. n-HA/Si-PA-SC@Ag characterized by TGA, FTIR, SEM/EDX, XRD, TEM, BET and ICP-AES techniques. Moreover, metal–ligand interactions in n-HA/Si-PA-SC@Ag complex models were assessed to make a quantitative representation for the immobilization behavior of Ag NPs on the surface of n-HA/Si-PA-SC through quantum chemistry computations. Furthermore, the performance of n-HA/Si-PA-SC@Ag was studied in the nitroarene, methylene blue and congo red reductions. Finally, the recyclability study as well as Ag-leaching verified that, n-HA/Si-PA-SC@Ag was stable and reused-up to four times without losing its activity.