The reaction of 2-methylpiperazine with the thiocyanate ligand and two transition metals leads to the production of two new isomorphous [ML2SCN4] where L is the 2-methylpiperazine and [M =Co (1), and Ni (2)], presenting an octahedral configuration. These compounds were characterized by single crystal X-ray crystallography, TG-DTA analysis, as well as infrared and UV-Vis spectroscopy and TG-DTA. The magnetic and antibacterial properties were also determined. Through the link with N-H···S hydrogen bonds, a global 3D network was established. The studied compounds show the metal center’s impact leading to different properties. Indeed, the first compound shows high spin orbit coupling, whereas the second one shows a weak antiferromagnetic interaction. The antibacterial activity is enhanced for the cobalt compound compared with the nickel compound and the DTA/TG curves show a phase transition for the nickel compound.