Periodontitis and severe trauma are major causes of damage to the periodontal ligament (PDL). Repairing the native conditions of the PDL is essential for the stability of the tissue and its interfaces. Bioprinting periodontal ligament stem cells (PDLSCs) is an interesting approach to guide the regeneration of PDL and interfacial integration. Herein, a collagen-based bioink mimicking the native extracellular matrix conditions and carrying PDLSCs was tested to guide the periodontal ligament organization. The bioink was tested at two different concentrations (10 and 15 mg/mL) and characterized by swelling and degradation, microstructural organization, and rheological properties. The biological properties were assessed after loading PDLSCs into bioinks for bioprinting. The characterization was performed through cell viability, alizarin red assay, and expression for ALP, COL1A1, RUNX2, and OCN. The in vivo biocompatibility of the PDLSC-laden bioinks was verified using subcutaneous implantation in mice. Later, the ability of the bioprinted PDLSC-laden bioinks on dental root fragments to form PDL was also investigated in vivo in mice for 4 and 10 weeks. The bioinks demonstrated typical shear-thinning behavior, a porous microstructure, and stable swelling and degradation characteristics. Both concentrations were printable and provided suitable conditions for a high cell survival, proliferation, and differentiation. PDLSC-laden bioinks demonstrated biocompatibility in vivo, and the bioprinted scaffolds on the root surface evidenced PDLSC alignment, organization, and PDLSC migration to the root surface. The versatility of collagen-based bioinks provides native ECM conditions for PDLSC proliferation, alignment, organization, and differentiation, with translational applications in bioprinting scaffolds for PDL regeneration.