In this paper, we have further developed our simple (one-pot) and rapid (short irradiation time) laser fabrication process of submicrometer spheres composed of amorphous calcium iron phosphate. In our previous process, laser irradiation was applied to a calcium phosphate (CaP) reaction mixture supplemented with ferric ions (Fe(3+)) as a light-absorbing agent. Because the intention of the present study was to fabricate magnetite-encapsulated CaP-based submicrometer spheres, ferrous ions (Fe(2+)) were used as a light-absorbing agent rather than ferric ions. The ferrous ions served as a light-absorbing agent and facilitated the fabrication of submicrometer and micrometer spheres of amorphous calcium iron phosphate. The sphere formation and growth were better promoted by the use of ferrous ions as compared with the use of ferric ions. The chemical composition of the spheres was controllable through adjustment of the experimental conditions. By the addition of sodium hydroxide to the CaP reaction mixture supplemented with ferrous ions, fabrication of CaP-based magnetic submicrometer spheres was successfully achieved. Numerous magnetite and wüstite nanoparticles were coprecipitated or segregated into the CaP-based spherical amorphous matrix via light-material interaction during the CaP precipitation process. The magnetic properties of the magnetite and wüstite formed in the CaP-based spheres were investigated by magnetization measurements. The present process and the resulting CaP-based spheres are expected to have great potential for biomedical applications.