The utilization of the silica-based materials in biomedical applications is evolving at a rapid pace with attentions mostly devoted to the ordered mesoporous silica nanoparticles (MSNs). However, apart from the ordered-MSNs, a range of other silica-based materials have been extensively applied in the controlled release (CR) of drugs, bone treatments, and bone regeneration, but have gained less attention. This article presents an overview on the recent research advancements of the silica-based materials, i.e., silica xerogels, silica microspheres, silica hybrids, silica microcapsule particles, silica ceramics, silica bioactive glasses, and silica beads which are mainly used in CR of drugs, bone disease treatments, and bone regeneration. The in vitro and in vivo biological evaluations on these silica-based materials for antibacterial properties, osteoblast cell activities, osteogenetic performances, cell adhesion and proliferation, bio-mineralization, and material degradation are discussed. The effect of morphology or surface modifications and addition of bone morphogenetic proteins to the silica-based formulations are illustrated.