Shell nacre from Pinctada species has been extensively researched for managing bone defects. However, there is a gap in the research regarding using shell nacre powder as a cement with improved biological and physicochemical properties. To address this, bone void filling cement was formulated by incorporating shell nacre powder and an organically modified ceramic resin (ormocer). The shell nacre powder was specifically processed from the shells of Pinctada fucata and analysed using thermogravimetric analysis (TGA), X-ray diffraction spectroscopy, Fourier transform infrared (FTIR), and Raman spectroscopy, confirming the presence of organic constituents and inorganic aragonite. Trace element analysis confirmed the eligibility of shell nacre powder for biomedical applications. Next, the ormocer SNLSM2 was synthesized through a modified sol–gel method. FTIR, Raman, TGA, and transmission electron microscopy studies revealed the presence of a ladder-structured siloxane backbone and methacrylate side chain. To develop chemical curable composite shell nacre cement (SNC), different amounts of shell nacre (24%, 48%, and 72%) were added to the SNLSM2 resin, and the impact on the physicochemical properties of the cement was studied. Among the compositions, SNC 72 exhibited significantly lower linear polymerization shrinkage (0.4%) and higher compressive (>100 MPa) and flexural strength (>35 MPa). SNC 72 was radiopaque, and the exotherm generated during the cement curing was minimal. Cytotoxicity studies with L929 cells revealed the non-cytotoxic nature of the cement. Overall, the findings of this study prove that the shell nacre cement is a promising candidate for managing bone voids.