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In regenerative bone tissue medicine, combining artificial bone substitutes with progenitor cells is a prospective approach. Surface modification via cold atmospheric plasma (CAP) enhances biomaterial–cell interactions, which are crucial for successful bone regeneration. Using a rabbit calvarial critical-size defect model, we assessed the use of CAP-pretreated beta-tricalcium phosphate (β-TCP), alone or with periodontal ligament stem cells (PDLSCs), for bone regeneration. Histological and histomorphometric analyses at two and four weeks revealed significantly improved bone regeneration and reduced inflammation in the CAP-treated β-TCP with PDLSCs compared to β-TCP alone. Immunohistochemical analysis also showed an increase in the bone healing markers, including bone morphogenic proteins 2 and 4, runt-related transcription factor 2, collagen-1, and osteonectin, after two and four weeks in the CAP-treated β-TCP implants with PDLSC. This in vivo study demonstrates for the first time the superior bone regenerative capacity of CAP-pretreated β-TCP seeded with PDLSCs, highlighting the therapeutic potential of this combined approach in osteoregeneration.