AbstractThree N‐substituted benzimidazole cobalt(II) complexes have been synthesized and fully characterized by elemental analysis, FT‐IR spectroscopy, and X‐ray crystallography. The crystal packing formation features were studied by AIM analysis, and the energy and nature of both weak noncovalent interactions in the crystal and metal–ligand coordination bonds were assessed. These N‐coordinated cobalt(II) complexes were screened for antimicrobial activities against Gram‐negative (Escherichia coli, Bacillus subtilis) and Gram‐positive (Enterococcus durans) bacteria. Minimal inhibitory concentrations (MIC = 6.2 mg/mL) were found for complex cobalt chloride with allylbenzimidazole ligands against E. durans and E. coli. Its antimicrobial activity is several times higher compared to the reference gentamicin. Molecular docking made it possible to consider the nature of binding of cobalt metal complexes with vinyl‐, allyl‐ and styrylbenzimidazole ligands to biological targets and estimate their energy. The binding energy meanings depend on protein and ligand type, and reaches 8 kcal/mol.