Novel pyrophosphate glass ceramic scaffolds (3D-Ca-P2) were fabricated and coated with several layers of CaO-P2O5-SiO2-MgO [3D-[Ca/P/Si]-XMg (X = 1,3 and 10 mol%)] as potential bioactive scaffolds for bone regeneration. The core scaffolds present a homogeneous distribution of polygonal grains consisting of 97% Ca2P2O7 with CaO-P2O5 glass as the matrix phase. Incorporating MgO into coatings led to extremely porous layers, assembled by nanosized equiaxed particles, which favoured the formation of different phases of tricalcium phosphate instead of pyrophosphate. Possible applications were determined based on Standard ISO/FDIS 23317:2014 for ceramics and powder samples. The 3D-Ca-P2 scaffolds’ non-bioactivity was modulated by coatings of different bioactivity behaviours depending on MgO contents. 3D-[Ca/P/Si]-10Mg was the best scaffold as precipitated hydroxyapatite (HA), was more amorphous than in the other scaffolds because Mg was incorporated into the HA network, which could favour subsequent cell adhesion. The multilayer scaffold provides advantages over others developed until now because in a unique structure all the characteristics required for an implant are combined. On a physical level, mechanical resistance, and porosity, and on a chemical level, a combination of calcium phosphate phases, similar to the mineral phase of bone, doped with Mg ions, which are capable of being transformed into HA in different periods of time.