The improvement of scaffold performances as cell carriers in a tissue implant is still a challenge in tissue engineering. Since cells in contact with a scaffold firstly sense its top surface before interacting with its macro-/micro-porous structure, the insertion of chemical motifs within the body of the scaffold could improve cell colonization through its entire structure. In this study, combinations of plasma deposition and treatment processes have been employed to create chemical gradients inside polycaprolactone porous scaffolds, whose micro-morphology has been finely characterized with synchrotron radiation computed micro-tomography. The graded chemical composition of these scaffolds has successfully allowed the increase of cell viability with respect to untreated materials. PCL scaffolds were produced with the solvent casting/particulate leaching and modified with low pressure plasma processes. SR Micro-CT images enabled a detailed morphological study of scaffolds, that together with chemical and wettability information, allowed to correlate scaffolding and plasma parameters to the scaffolds properties. A combination of high porosity and hydrophilicity led to improved adhesion of osteoblast cells on scaffolds in vitro.