Black seed (Nigella sativa [NS]) is used in traditional medicine as an antibacterial agent. In this study, novel hybrid scaffolds were manufactured from poly(ɛ‐caprolactone[PCL])/ Poly(lactic acid [PLA]) with NS extract by double‐nozzle electrospinning for wound healing application. Optimal conditions were found using response surface methodology including feed rate 0.8 ml/hr, voltage 20 kV and PLA 8% /PCL 10% concentrations. The effect of NS extract on the properties of the scaffold was evaluated by scanning electron microscopy, contact angle, and mechanical test. The PLA‐PCL/NS 20% beadles, and smooth nanofibrous web was obtained as the optimum scaffold with an average diameter of 638 ± 69 nm and the contact angle of 44°. In addition, the biological properties of the scaffolds such as antibacterial against Staphylococcus aureus (gram‐positive) and Escherichia coli (gram‐negative) bacteria, MTT assay, extract release, and cell growth (human mesenchymal stem cells) were examined. Incorporation of NS extract into the nanofibers caused to enhance the biological properties, cell viability and cell proliferation without toxicity.