Herein, the synthesis and antimicrobial activities of [Mn(MorphBPT)(H2O)2NO3]NO3; (1) and [Mn(PipBPT)(H2O)2NO3]NO3; (2) complexes of the pincer-type tridentate ligands MorphBPT; 4-(4,6-di(1H-pyrazol-1-yl)-1,3,5-triazin-2-yl)morpholine and PipBPT; 2-(piperidin-1-yl)-4,6-di(1H-pyrazol-1-yl)-1,3,5-triazine are presented. Both complexes have slightly distorted octahedral coordination geometry. Their molecular packing depends on O–H···O, C–H···O hydrogen bonds and anion–π stacking contacts. Hirshfeld analysis was used to quantify the different contacts. Both complexes exhibited better anti-fungal activity than the standard Fluconazole and comparable antibacterial activity to Gentamycin against Staphylococcus aureus and Escherichia coli microbes. Moreover, complexes 1 and 2 are biologically more active than the free ligands against these microbes.