The title compound, [Co(C10H10BF6N4)(C15H13BF9N6)], is a polymorph of the previously reported neutral cobalt(II) complex [Stibrany & Potenza (2010 ▶). Acta Cryst. E66, m506–m507], which contains one each of the monoanionic ligands, bis[5-methyl-3-(trifluoromethyl)pyrazol-1-yl]borate (Bp) and tris[5-methyl-3-(trifluoromethyl)pyrazol-1-yl]borate (Tp). A distorted octahedral coordination geometry of the CoII atom results from ligation of an H atom, which is part of an agostic B—H⋯Co interaction [H⋯Co = 2.12 (3) Å], and by five imine N atoms, two from a Bp ligand and three from a Tp ligand. Weak intra- and intermolecular C—F⋯π interactions with F⋯centroid distances ranging from 3.025 (4) to 3.605 (4) Å are observed.