A series of new Co(II), Cu(II), and Mn(II) complexes containing both aromatic and aliphatic organofluorine species were obtained in 76–90% yields. Structural properties of these coordination compounds derived from pentafluorophenyl-substituted 3-(2-pyridyl)-1,2,4-triazine, 2,2′-bipyridine and hexafluoroacetylacetonate ligands were comprehensively studied using by XRD analysis, with the slightly distorted octahedral coordination being revealed in all cases. The spatial characteristics for 3-(2-pyridyl)-1,2,4-triazine bearing pentafluorophenyl moiety at C(5) position as well as its bipyridine analog in relation to ones for the corresponding metal complexes were also studied. The revealed structural features for the elaborated Co(II), Cu(II), and Mn(II) complexes based on 2,2′-bipyridine and 3-(2-pyridyl)-1,2,4-triazine ligands containing organofluorine species could be of particular interest in the design of advanced materials for catalysis, chemosensory, molecular electronics, and other fields of materials science.