The controlled delivery of selenium nanoparticles (Se‐NPs) is promising for bone cancer treatment due to their dual benefits in bone regeneration and tumor inhibition, yet achieving an optimal dosing regimen remains challenging. Natural mesoporous biosilica (BS) beads have shown promise for drug delivery due to their microporous structure. This study explores incorporating BS beads into collagen‐chitosan (Coll‐CS) scaffolds, known for bone repair, to control Se‐NP delivery. Two approaches are compared: loading Se‐NPs into BS beads before integrating them into Coll‐CS scaffolds versus directly loading Se‐NPs into Coll‐CS scaffolds. The scaffold properties, Se release kinetics, cytocompatibility, and effects on mesenchymal stem cells (MSCs) and prostate cancer cells (LNCaP) are evaluated. BS bead‐loaded scaffolds provide controlled Se‐NP release and enhanced mechanical properties compared to directly loaded scaffolds. Higher Se‐NP concentrations in BS‐loaded scaffolds effectively promote MSC osteogenic differentiation and mineralisation while inhibiting LNCaP cell viability. In contrast, low Se‐NP concentrations not only induce early osteogenic differentiation but also promote cancer cell proliferation, underscoring the need for optimal Se‐NP concentration and release. These findings suggest that BS bead‐loaded Coll‐CS scaffolds are a promising strategy for controlled Se‐NP delivery, addressing the dual challenges of bone formation and cancer recurrence prevention in bone cancer treatment.