Fused deposition modeling (FDM) is a three-dimensional (3D) printing technology typically used in tissue engineering. However, 3D-printed row scaffolds manufactured using material extrusion techniques have low cell affinity on the surface and an insufficient biocompatible environment for desirable tissue regeneration. Thus, in this study, plasma treatment was used to render surface modification for enhancing the biocompatibility of 3D-printed scaffolds. We designed a plasma-based 3D printing system with dual heads comprising a plasma device and a regular 3D FDM printer head for a layer-by-layer nitrogen plasma treatment. Accordingly, the wettability, roughness, and protein adsorption capability of the 3D-printed scaffold significantly increased with the plasma treatment time. Hence, the layer-by-layer plasma-treated (LBLT) scaffold exhibited significantly enhanced cell adhesion and proliferation in an in vitro assay. Furthermore, the LBLT scaffold demonstrated a higher tissue infiltration and lower collagen encapsulation than those demonstrated by a non-plasma-treated scaffold in an in vivo assay. Our approach has great potential for various tissue-engineering applications via the adjustment of gas or precursor levels. In particular, this system can fabricate scaffolds capable of holding a biocompatible surface on an entire 3D-printed strut. Thus, our one-step 3D printing approach is a promising platform to overcome the limitations of current biocompatible 3D scaffold engineering.