Cell colonization of the surrounding environment is a very significant process in both physiological and pathological events. In order to understand the tissue regeneration process and thereby provide guidance principles for designing new biomaterials, it is of paramount importance to study the cell colonization in the presence of physical, chemical, and biological cues. Flat "gradient" materials are generally used with this purpose. Three dimensional gradient scaffolds mimicking more precisely the situation in vivo are somewhat more complex to fabricate and characterize. Scaffolds for Tissue Engineering (TE) made of hydrophobic synthetic polymers do not allow good cell colonization: far from their periphery, in fact, internal cell colonization is usually low. In this research poly-ε caprolactone (PCL) scaffolds have been "decorated" with chemical gradients both on top and along their thickness by means of cold plasma processes, in order to improve cell colonization of their core. Plasma treatments with a mixture of argon and oxygen (Ar/O), as well as plasma deposition of differently cross-linked poly(ethylene oxide) (PEO)-like coatings, have been performed. This study establishes that cross-linked PEO-like domains interspaced with native PCL ones deposited only on top of the scaffold (i.e., coating that penetrates less than 300 μm inside the scaffold) are more effective in promoting cell colonization across the scaffolds than the other tested materials including superhydrophilic samples and that ones produced by tested double step approaches. Last but not least, one result of this research is that, in the case of plasma coatings with low deposition rates and porous materials with a low pore interconnectivity, it is possible to improve penetration of low pressure plasma active species inside the scaffold's core thorough a pretreatment of the porous materials (i.e., penetration up to 4500 mm far from topside).