Here, we demonstrated the fabrication of a composite scaffold (chitosan [CS], collagen [Col], and hydroxyapatite [HA]) with the incorporation of encapsulated Cissus quadrangularis (CQ) extract for tissue engineering applications. First, the crude extract of CQ loaded nanoparticles were synthesized via double emulsion technique using polycaprolactone (PCL) and polyvinyl alcohol (PVA) as oil and aqueous phases, respectively. Both PCL (20, 40, and 80 mg/mL) and PVA (0.5%, 1%, and 3% w/v) concentrations were varied to determine the optimum concentrations for CQ-loaded nanoparticle preparation. The CQ-loaded PCL nanoparticles (CQ-PCL NPs), prepared with 20 mg/mL PCL and 0.5% (w/v) PVA, exhibited the smallest size of 334.22 ± 43.21 nm with 95.54 ± 1.49% encapsulation efficiency. Then, the CQ-PCL NPs were incorporated into the CS/Col/HA scaffolds. These scaffolds were also studied for their ultrastructure, pore sizes, chemical composition, compressive modulus, water swelling, weight loss, and biocompatibility. The results showed that the addition of CQ-PCL NPs into the scaffolds did not dramatically alter the ultrastructure and properties of the scaffolds, compared to CS/Col/HA scaffolds alone. However, incorporation of CQ-PCL NPs in the scaffolds improved the release profile of CQ by preventing the initial burst release and prolonging the release rate of CQ. In addition, the CQ-PCL NPs-loaded CS/Col/HA scaffolds supported the attachment and proliferation of MC3T3-E1 osteoblast cells.