Applying biologically active scaffolds to promote bone tissue regeneration and reduce environmental pollution caused by biological waste are the main goals of this study. Sol-gel methods were utilized in this study to create nano-sized bioactive glass ceramics, which are frequently used as graft material or bone filler. Two synthesis routes were compared: one utilizing pure chemicals and the other utilizing biogenic CaCO₃ sourced from eggshell waste as an innovative approach. X-ray diffraction and Fourier transform infrared analyses showed that both bioglass powders consisted of amorphous phases with particle sizes of crystals measuring 14–16 nm, as observed through transmission electron microscopy. Upon immersion in phosphate-buffered saline, carbonate apatite crystals were observed to develop on the surfaces of solid bioglass and composite polymeric scaffolds composed of polycaprolactone/zein protein. These porous and non-toxic scaffolds facilitated osteoblast attachment, proliferation, and differentiation. The incorporation of bioglass enhanced mechanical properties, rates of biodegradation, and cell behavior. Incorporating biogenic bioglass powder into the PCL/Zein scaffold matrix improved the thermal stability of the synthesized scaffolds. Biogenic bioglass contributed to the bioactivity, degradation rate, viability, and calcium deposition of bone marrow Mesenchymal stem cells (r-BMMSC) to a certain extent. This study explores the utilization of eggshell waste as a cost-effective source of calcium for Nano-bioglass synthesis. The resulting nano-bioglass was incorporated into 3D PCL/Zein composite scaffolds for bone tissue engineering in non-load-bearing areas. Furthermore, the study suggests the application of biogenic bioglass in dentistry for oral care product fabrication due to its superior bioactivity compared to chemically synthesized bioglass.