A challenge for tissue engineering is to produce synthetic scaffolds of adequate chemical, physical, and biological cues effectively. Due to the hydrophobicity of the commonly used synthetic polymers, the printed scaffolds are limited in cell-seeding and proliferation efficiency. Furthermore, non-uniform cell distribution along the scaffolds with rare cell attachment in the core region is a common problem. There are no available commercial systems able to produce multi-type material and gradient scaffolds which could mimic the nature tissues. This paper describes a plasma-assisted bio-extrusion system (PABS) to overcome the above limitations and capable of producing functional-gradient scaffolds; it comprises pressure-assisted and screw-assisted extruders and plasma jets. A hybrid scaffold consisting of synthetic biopolymer and natural hybrid hydrogel alginate-gelatin (Alg-Gel) methacrylate anhydride, and full-layer N2 plasma modification scaffolds were produced using PABS. Water contact angle and in vitro biological tests confirm that the plasma modification alters the hydrophilicity properties of synthetic polymers and promotes proliferation of cells, leading to homogeneous cell colonization. The results confirm the printing capability for soft hard material integration of PABS and suggest that it is promising for producing functional gradient scaffolds of biomaterials.