A new Co(II) perchlorate complex of the bis-morpholino/benzoimidazole-s-triazine ligand, 4,4′-(6-(1H-benzo[d]imidazol-1-yl)-1,3,5-triazine-2,4-diyl)dimorpholine (BMBIT), was synthesized and characterized. The structure of the new Co(II) complex was approved to be [Co(BMBIT)2(H2O)4](ClO4)2*H2O using single-crystal X-ray diffraction. The Co(II) complex was found crystallized in the monoclinic crystal system and P21/c space group. The unit cell parameters are a = 22.21971(11) Å, b = 8.86743(4) Å, c = 24.38673(12) Å and β = 113.4401(6)°. This heteroleptic complex has distorted octahedral coordination geometry with two monodenatate BMBIT ligand units via the benzoimidazole N-atom and four water molecules as monodentate ligands. The hydration water and perchlorate ions participated significantly in the supramolecular structure of the [Co(BMBIT)2(H2O)4](ClO4)2*H2O complex. Analysis of dnorm map and a fingerprint plot indicated the importance of O···H, N···H, C···H, C···O, C···N and H···H contacts. Their percentages are 27.5, 7.9, 14.0, 0.9, 2.8 and 43.5%, respectively. The sensitivity of some harmful microbes towards the studied compounds was investigated. The Co(II) complex has good antifungal activity compared to the free BMBIT which has no antifungal activity. The Co(II) complex has good activity against B. subtilis, S. aureus, P. vulgaris and E. coli while the free BMBIT ligand has limited activity only towards B. subtilis and P. vulgaris. Hence, the [Co(BMBIT)2(H2O)4](ClO4)2*H2O complex has broad spectrum antimicrobial action compared to the free BMBIT ligand.