Supercritical foaming allows for the solvent-free processing of synthetic scaffolds for bone regeneration. However, the control on the pore interconnectivity and throat pore size with this technique still needs to be improved. The use of plasticizers may help overcome these limitations. Eugenol, a GRAS natural compound extracted from plants, is proposed in this work as an advanced plasticizer with bioactive properties. Eugenol-containing poly(ε-caprolactone) (PCL) scaffolds were obtained by supercritical foaming (20.0 MPa, 45 °C, 17 h) followed by a one or a two-step depressurization profile. The effects of the eugenol content and the depressurization profile on the porous structure of the material and the physicochemical properties of the scaffold were evaluated. The combination of both processing parameters was successful to simultaneously tune the pore interconnectivity and throat sizes to allow mesenchymal stem cells infiltration. Scaffolds with eugenol were cytocompatible, presented antimicrobial activity preventing the attachment of Gram positive (S. aureus, S. epidermidis) bacteria and showed good tissue integration.