Three new CoII-coordination polymers (Co-CPs) containing glutarates and bipyridyl ligands, formulated as [Co2(Glu)2(µ-bpa)2]·(H2O)4 (1), [Co4(Glu)4(µ-bpp)2] (2), and [Co2(Glu)2(µ-bpe)2]·(H2O)0.5 (3), were prepared, and their structures were determined by X-ray crystallography. Glutarates bridge CoII ions to form 2D sheets, and the sheets are connected either by bpa or by bpp ligands to form 3D networks 1 and 2, respectively. Both frameworks 1 and 2 are two-fold interpenetrated, and there is no significant void volume in either network. Four glutarates bridge two CoII ions to form chains, and these chains are connected by bpe ligands to form the 2D sheet 3. The antifungal properties of these new Co-CPs were tested against two model fungal pathogens, Candida albicans and Aspergillus niger. Under the maximum concentration of Co-CPs, 2.0 mg mL−1, the inhibition rates of Co-CPs against A. niger were much lower (44–62%) than those (90–99.98%) observed in C. albicans. The results indicate that 1–3 can inactivate C. albicans cells more efficiently than A. niger spores in the same treatment time, and the greater inactivation of C. albicans can be explained by dramatic changes in the morphology of C. albicans cells. We also found that Co-CPs could generate the reactive species NO and H2O2, and these species might play a role in inactivating fungal cells. Additionally, degradation tests confirmed that the leaching of CoII ions from Co-CPs was not significant. The small amount of leached CoII ions and the robust Co-CPs themselves as well as the reactive species generated by Co-CPs can actively participate in fungal inactivation.