Injectable pastes based on bioactive compounds and natural polymers are of interest in non-invasive bone surgeries. Several quantities of quercetin (100, 150, and 200 μM) were added to a sol-gel derived mesoporous bioactive glass. Injectable pastes based on quercetin-loaded bioactive glass, sodium alginate, and hyaluronic acid were prepared. Aggregated nanoparticles of bioactive glass and quercetin-loaded bioactive glass with mesoporous morphologies were confirmed by TEM and BET techniques. The quercetin release study was assessed in phosphate-buffered solution medium over 200 h and the obtained data were fitted by different eqs. A sustained release of quercetin was found, in which a better regression coefficient was achieved using Weibull equation. Human-derived mesenchymal stem cells were utilized to determine alkaline phosphatase activity and bone-related protein expression by western blotting and real-time PCR evaluations. Quercetin-loaded pastes increased the levels of alkaline phosphatase activity and the expression of Collagen-1, Osteopontin, Osteocalcin, and Runx2 proteins in a concentration-dependent manner. Due to the mesoporous architecture and high specific surface area of bioactive glass, the paste made of these particles and sodium alginate/hyaluronic acid macromolecules is appropriate matrix for quercetin release, resulting in promoted osteogenesis. The further in vivo studies can support the osteogenesis capacity of the quercetin-loaded paste.