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Mesoporous silica‐based materials are currently being explored as a new type of bioscaffold for bone regeneration applications. Zinc(Zn) ion incorporation is shown to play an important role in promoting bone regeneration and also providing antimicrobial activity to the scaffold materials. In this work, the role of pore size, geometry, and ordered structure on the Zn loading and release performance of two different mesoporous silica, SBA‐1 and SBA‐15, are compared. Zn loading is varied from 2.5 to 10 wt% for both samples, and its effect on the antibacterial and osteogenic activity is evaluated. Zn loading up to 10 wt% has a negligible effect on the morphology and textural properties of the mesoporous silica samples. The inductively coupled plasma mass spectrometry (ICP‐MS) analysis reveals that SBA‐15 exhibits significantly higher Zn release in Luria‐Bertani (LB) broth as compared to SBA‐1 that is reflected in the higher antibacterial activity of SBA‐15 against both gram‐positive and gram‐negative bacteria. Various assays show that 5 wt% Zn loading is sufficient to produce both bactericidal and inhibitory effects on bacterial cells. The 5 wt% Zn‐loaded samples induce osteogenic differentiation ofavianized bone marow‐derived stromal cells (TVA‐BMSCs) though SBA‐15 samples show better compatibility compared to SBA‐1, suggesting that Zn incorporation can produce sufficient antibacterial effect and osteogenic differentiation of TVA‐BMSCs. [ABSTRACT FROM AUTHOR]