Here the role of secondary ligands and their hydrogen bonding patterns in determining the photoluminescence quantum yields of aminopyrazine (ampyz) coordination polymers was probed. The acetate present in the highly efficient blue-light-emitting cadmium-ampyz coordination polymer was replaced with nitrate, and another ampyz coordination polymer with Zn(NO3)2 was also synthesized. The replacement of the acetate with nitrate yielded another cadmium coordination polymer with high blue-light iPLQY and ePLQY values of 11.2% and 10.0%, respectively, whereas the zinc coordination polymer exhibited quantum yields of about 6%. The same ampyz bidentate coordination backbone that was reported in a compound in the literature was observed in the two compounds reported here. However, four water molecules complete the zinc octahedral coordination environment and nitrate engages only one of its oxygens in coordination with Cd2+ rather than both in the case of acetate, resulting in lower molecular constraint and poor orbital overlap. These direct features of the secondary ligand, together with less and weaker intramolecular hydrogen-bonded motifs in both [Cd(ampyz)(NO3)(H2O)2]n(NO3)n·nH2O and [Zn(ampyz)(H2O)4]n(NO3)2n·2nH2O prepared here, are responsible for the decay of the photoluminescence efficiency, which should be further accounted for in the design of novel improved high-efficiency fluorescent compounds.