As a result of their close similarities to the inorganic mineral components of human bone, hydroxyapatite nanoparticles (n-HAp) are widely used in biomedical applications and for the elaboration of biocompatible scaffold drug delivery systems for bone tissue engineering. In this context, a new efficient and economic procedure was used for the consolidation of n-HAp in the presence of various Nigella sativa (NS) fractions at a near-room temperature. The research conducted in the present study focuses on the physicochemical properties of loaded n-HAp 3D scaffolds by NS fractions and the in vitro antibacterial activity against Gram-negative (Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, Klebsiella pneumoniae ATCC 27853), and Gram-positive (Staphylococcus aureus ATCC 29213, Enterococcus faecalis ATCC 700603) bacteria. In order to better understand the effect of the inserted fractions on the HAp molecular structure, the elaborated samples were subject to Fourier transform infrared (FTIR) and X-ray diffraction (XRD) spectroscopic analyses. In addition, the morphological investigation by scanning electron microscope (SEM) of the loaded n-HAp 3D scaffolds demonstrated the presence of a porous structure, which is generally required in stimulating bone regeneration. Furthermore, the fabricated 3D composites exhibited significant antibacterial activity against all tested bacteria. Indeed, MIC values ranging from 5 mg/mL to 20 mg/mL were found for the HAp-Ethanol fraction (HAp-Et) and HAp-Hexane fraction (HAp-Hex), while the HAp-Aqueous fraction (HAp-Aq) and HAp-Methanol fraction (HAp-Me) showed values between 20 mg/mL and 30 mg/mL on the different strains. These results suggest that the HAp-NS scaffolds were effective as a drug delivery system and have very promising applications in bone tissue engineering.