Laser Ca3(VO4)2 single crystals (СVO; space group R3c, Z = 21) with crystallochemical formula Ca118Ca218Ca318Ca46(Ca5 + Са5А)3(V118V218V36)O168 grown by the Czochralski method were doped with Мn2O3 (CVO:Мn2O3) and Сo3O4 (CVO:Co3O4) by high-temperature diffusion annealing. Statistical and local structures were comprehensively studied by single-crystal and powder synchrotron X-ray diffraction and conventional single-crystal X-ray diffraction as well as by X-ray absorption spectroscopy for the first time. The presence of Mn(2+δ)+ ions with a mixed formal charge and Co2+ ions in the Ca2 (monocapped trigonal prism), Ca3 (two-capped trigonal prism), and Ca4 (octahedron) sites was revealed by diffraction methods. The tetrahedral coordination and the coordination intermediate between tetrahedral and octahedral were established for Mn(2+δ)+ and Co2+ ions, respectively. A fundamentally different structural behavior of dopant ions (concentration, formal charge, and coordination environment) in the CVO crystals doped with manganese in the form of Mn2O3 during the crystal growth or by high-temperature diffusion annealing was observed. The relationship between characteristic bands in the absorption, fluorescence, and excitation spectra of CVO:Мn2O3 and CVO:Co3O4 samples and transition metals with specific formal charges is discussed.