Producing synthetic scaffolds with adequate physical, chemical, and biological properties remains a challenge for tissue engineering. Internal architecture, surface chemistry, and material properties have strong impact on the cell biological behavior. This requires sophisticated systems not only able to process multiple materials with different characteristics, creating fully interconnected 3D porous structures with high reproducibility and accuracy, but also able to modify their properties during the fabrication process. This study introduces a novel additive manufacturing system comprising a multiprinting unit (screw-assisted and pressure-assisted printing heads) together with a plasma unit that enables the surface modification of printed scaffolds. Poly(ɛ-caprolactone) scaffolds with a lay-down pattern of 0/90° were fabricated using the screw-assisted printing head and a plasma jet unit used to uniformly modify each layer, a specific region of each layer during the printing process or the external surface of the printed scaffolds. Scaffolds were produced using different plasma exposure times and different distance between the plasma head and the printed layer, and fixed printing conditions. Produced scaffolds were morphologically, mechanically, chemically, and biologically characterized. Results show that the distance between the plasma head and the printed material has no significant effect on the mechanical properties, whereas the increase of the plasma deposition velocity increases the mechanical properties. As expected, plasma treatment increases hydrophilicity and consequently the biological performance of the scaffolds. Results also show the potential of the proposed fabrication system to create functional gradient or scaffolds with tailored properties.