Regenerative medicine is an emerging discipline that investigates the possibilities of restoring portions of damaged biological tissues in a controlled way. An interesting practice in this field consists in the implantation of biomimetic scaffolds colonized by mesenchymal stem cells taken from the patient. In this work, a set of design guidelines for customized biomimetic scaffolds was analyzed, and a full procedure aimed at implementing them for the treatment of a real clinical case was outlined. In detail, a highly sustainable and biocompatible material obtained from chemical processing of fish industry by-products was selected. The primary phases of the proposed design procedure consisted in biomedical data acquisition, parametric modelling of the damaged region to regenerate, structural design of the scaffold based on the avoidance of stress shielding effects, and evaluation of the physiological pressure to apply on the implanted porous construct to maximize mature bone formation. The presented procedure resulted as an effective practice for the design of personalized biomimetic scaffolds for tissue regeneration, thus providing at the same time many insights towards novel sustainable design solutions in biomedical fields.