Developing a delivery system has become crucial in engineering cutting-edge next-generation theranostic approaches. Therefore, in the present research work, a customized Mesoporous silica nanoparticle (MSiNPs) was designed by adapting the Stöber method with silane polymerization for Morin (MO) adsorption. The average size of MSiNPs was 50–130 nm as measured by TEM, while FE-SEM revealed a spherical surface shape. According to Raman and FTIR spectra, while the synthesis of MSiNPs, CTAB (a surfactant) was eliminated from MSiNPs, silane was functionalized, and with a loading efficiency of 10.28 ± 0.22%, MO was adsorbed. Molecular docking was used to perform in-silico studies to investigate the interaction of native MO with antidiabetic and antioxidant enzymes. Furthermore, the antioxidant and antidiabetic effects of both MO adsorbed MSiNPs, and native MO were examined in vitro, with the former showing promise even at lower concentrations than the latter. The cell survival experiment on Mouse macrophages RAW 264.7 and HCT cells revealed that MO adsorbed MSiNPs were nontoxic up to 15 μg/ml. The acute toxicity of different concentrations of MO adsorbed MSiNPs was also conducted in an in vivo model zebrafish (Danio rerio), where the study was conducted for about 96 h and evaluated for histological significance. The findings described above revealed that the MSiNPs were electrochemically, structurally, and thermally stable and MO adsorbed MSiNPs were nontoxic and biocompatible, implying that it might be an effective drug delivery vehicle for MO in the future. Moreover, in coming times, this nano-delivery system with effective biodistribution of the adsorbed MO could be explored as an antidiabetic and anti-cancer agent.