AbstractMorbidities associated with natural bone have highlighted the need of advanced bioactive implants for the replacement of damaged bone. Known for their beneficial bioactivity and biocompatibility, Nigella sativa seeds (kalonji/black seed) are traditionally used in many medications. This research focuses on the positive impact of black seed extract on the chondroitin sulfate‐based hydroxyapatite nanocomposite for bone tissue regeneration applications. Novel nanocomposites with varied concentrations of black seed extract (0, 1, 2, and 3 wt%) were fabricated through a coprecipitation approach and analyzed for physicochemical and biological applications. The results of X‐ray diffraction and FTIR spectroscopy revealed that the HCSK3 nanocomposite was successfully developed with appreciably strong molecular interactions among their components. HCSK3 nanocomposite exhibits higher rough surface morphology (Ra −1.13 µm and Rz −4.8 µm), uniform particle distribution (average particle size −9.9 nm), and good thermal stability with total weight loss of 13%. It also provides better nucleation sites for apatite formation and protein adsorption stimulating cell attachment, proliferation, and differentiation. Moreover, HCSK3 nanocomposite showed excellent cell viability, higher ARS/ALP activities, better antibacterial property, and nonhemolytic property (below 3%). Thus, it can be concluded that HCSK3 nanocomposite manifested the highest biocompatibility and negligible cell toxicity. Therefore, it can be employed as an ideal bone implant in the bone tissue restoration phenomenon.