Abstract: Objectives A new strategy in the field of regenerative bone tissue medicine involves the combination of artificial bone substitutes and progenitor cells. In this approach the positive interaction of biomaterials and cells is crucial for successful bone regeneration. Materials and methods Herein, we examined if cold atmospheric plasma (CAP)-pretreated beta-tricalcium phosphate (β-TCP) alone, or in combination with periodontal ligament stem cells (PDLSCs), increases the bone regeneration in rabbit calvarial critical-size defect model. After two and four weeks of bone regeneration we analyzed and compared the bone formation in experimental groups using histology and histomorphometry. In addition, we used immunohistochemistry to analyze the protein expression of bone healing markers. Results After two and four weeks of bone regeneration, the results of histological and histomorphometric, analysis demonstrated significantly higher bone regeneration capacity and absence of inflammatory reaction in the implant of plasma-treated β-TCP in combination with PDLSCs compared to the β-TCP alone. Furthermore, immunohistochemical analysis showed the highest percentages of immunostained cells for the bone healing markers, bone morphogenic proteins 2 and 4, runt-related transcription factor 2, collagen-1, and osteonectin in the defects filled with CAP-treated β-TCP and PDLSC which additionally support beneficial therapeutic effects of such combined approach on osteoregeneration. Conclusion The CAP-pretreated β-TCP implant seeded with PDLSCs shows significantly higher bone regeneration capacity and absence of inflammatory reaction in vivo in comparison to the β-TCP alone. Clinical relevance Cold atmospheric plasma could be an effective method of treating β-TCP to improve the interaction of the material with stem cells enhancing regeneration of the bone.