A two-dimensional (2D) cobalt(ii) metal-organic framework (MOF) constructed by a ditopic organic ligand, formulated as {[Co(Hbic)(H2O)]·4H2O}n (1) (H2bic = 1H-benzimidazole-5-carboxylic acid), was hydrothermally synthesized and structurally characterized. Single-crystal X-ray diffraction shows that the distorted octahedral Co2+ ions, as coordination nodes, are bridged to form 2D honeycomb networks, which are further organized into a 3D supramolecular porous framework through multiple hydrogen bonds and interlayer π-π interactions. Dynamic crystallography experiments reveal the anisotropic thermal expansion behavior of the lattice, suggesting a flexible hydrogen-bonded 3D framework. Interestingly, hydrogen-bonded (H2O)4 tetramers were found to be located in porous channels, yielding 1D proton transport pathways. As a result, the compound exhibited a high room-temperature proton conductivity of 1.6 × 10−4 S cm−1 under a relative humidity of 95% through a Grotthuss mechanism. Magnetic investigations combined with theoretical calculations reveal giant easy-plane magnetic anisotropy of the distorted octahedral Co2+ ions with the experimental and computed D values being 87.1 and 109.3 cm−1, respectively. In addition, the compound exhibits field-induced slow magnetic relaxation behavior at low temperatures with an effective energy barrier of Ueff = 45.2 cm−1. Thus, the observed electrical and magnetic properties indicate a rare proton conducting SIM-MOF. The foregoing results provide a unique bifunctional cobalt(ii) framework material and suggest a promising way to achieve magnetic and electrical properties using a supramolecular framework platform. © 2023 The Royal Society of Chemistry.