Two new paramagnetic hybrid cobalt(II)-hexaborate(2-)-based semi-organic complexes: (2A3MP)2[Co{κ3O–B6O7(OH)6}2].2H2O (1) and (2A4MP)2[Co{κ3O–B6O7(OH)6}2].2H2O (2) (2A3MP = 2-amino-3-methylpyridinium, 2A4MP = 2-amino-4-methylpyridinium) have been obtained and characterized by X-ray diffraction, FT-IR, TG–DTA, optical and magnetic measurements. X-ray diffraction revealed two isostructural compounds based on Co(II) complexes of bis(κ3O-donor hexaborate(2-)) ligands, [Co{κ3O–B6O7(OH)6}2]2−, differing only in the organic counter cation. The hydrated oxidopolyborate anions are extensively H-bounded to form 3D-porous supramolecular anionic frameworks. In both 1 and 2 isostructures, 2A3MP and 2A4MP cations are present in the created voids of the inorganic frameworks through a set of H-bonds with 58.5 and 60.5% H…O/O…H intercontact contributions, respectively, for 1 and 2 as confirmed by Hirshfeld surfaces analysis. The optical band gap of Co(II) complexes ranges between 2.72 and 2.82 eV. Both compounds exhibited well-resolved paramagnetic properties with magnetic susceptibility values ranging between 0.9552 cm3 mol−1 (at 2 K) and 0.0088 cm3 mol−1 (at 300 K), typical of octahedral Co(II) complexes.