Multiphasic scaffolds that combine different architectural, physical, and biological properties are the best option for the regeneration of complex tissues such as the periodontium. Current developed scaffolds generally lack architectural accuracy and rely on multistep manufacturing, which is difficult to implement for clinical applications. In this context, direct-writing electrospinning (DWE) represents a promising and rapid technique for developing thin 3D scaffolds with controlled architecture. The current study aimed to elaborate a biphasic scaffold using DWE based on two polycaprolactone solutions with interesting properties for bone and cement regeneration. One of the two scaffold parts contained hydroxyapatite nanoparticles (HAP) and the other contained the cementum protein 1 (CEMP1). After morphological characterizations, the elaborated scaffolds were assessed regarding periodontal ligament (PDL) cells in terms of cell proliferation, colonization, and mineralization ability. The results demonstrated that both HAP- and CEMP1-functionalized scaffolds were colonized by PDL cells and enhanced mineralization ability compared to unfunctionalized scaffolds, as revealed by alizarin red staining and OPN protein fluorescent expression. Taken together, the current data highlighted the potential of functional and organized scaffolds to stimulate bone and cementum regeneration. Moreover, DWE could be used to develop smart scaffolds with the ability to spatially control cellular orientation with suitable cellular activity at the micrometer scale, thereby enhancing periodontal and other complex tissue regeneration.