A challenge for tissue engineering is to produce synthetic scaffolds of adequate chemical, physical and biological cues effectively. This paper describes a plasma-assisted bio-extrusion system (PABS) to produce functional-gradient scaffolds; it comprises pressure-assisted and screw-assisted extruders, and plasma jets. A hybrid scaffold consisting of synthetic biopolymer and natural hydrogel was produced using PABS. This paper also describes full-layer plasma modification scaffold fabrication with 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 suggest this system is promising for producing functional gradient scaffolds of biomaterials.