Considerable effort in the field of periodontal tissue engineering has been expended in the construction of advanced biomatrix for the treatment of periodontal diseases caused by poor oral hygiene, malnutrition, genetic factors, and systemic disorders. With these in mind, the ultimate goal of this investigation is to fabricate sophisticated scaffolds using jellyfish collagen (JC) and aqueous Salvadora persica (Miswak) extracts. Rhizostoma pulmo species JC was isolated and characterized in depth. Miswak was extracted using two different methods. The extraction yield was calculated to be 14.2 ± 0.9% and 17.1 ± 0.4% for Methods I and II, respectively. Gas chromatography-mass spectroscopy (GC-MS) results revealed the extract to be composed of 1,8-cineole (49.3%), benzyl nitrile (36.2%), benzyl isothiocyanate (5.9%), limonene (2.4%), eugenol (0.8%), and palmitic acid (0.3%). Total phenolic content and antioxidant capacities of the extracts were also determined by spectrophotometric means. Human periodontal ligament fibroblast cells were isolated and expanded. Cell viability on JC and miswak extract-laden JC scaffolds was determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium Bromide (MTT) assay. Microarchitectures of the JC, 0.05 and 0.1% miswak extract-laden JC scaffolds and also cellular behaviors on these surfaces were evaluated by scanning electron microscopy (SEM) analysis. This study suggests that miswak extract-laden JC scaffolds would present new opportunities for periodontal tissue engineering.