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Grain yield (GY) and grain protein content (GPC) are important traits for wheat breeding and production; however, they are usually negatively correlated. The Q gene is the most important domestication gene in cultivated wheat because it influences many traits, including GY and GPC. Additionally, Qc1 is an overexpressed Q allele containing a missense mutation in the microRNA172-binding site. The common wheat (Triticum aestivum) mutant S-Cp1-1, which carries Qc1, has a very high GPC and some unfavorable characteristics, including dwarfism and compact spikes, which decrease the GY. We previously suggested that missense mutations in the sequences encoding the AP2 domains of Qc1 can be exploited to enhance the agronomic performance of wheat. In this study, we characterized two new Q alleles (Qs1 and Qc1-N8). Compared with the wild-type Q allele, Qs1 contains a missense mutation in the sequence encoding the first AP2 domain, whereas Qc1-N8 has two missense mutations, one in the sequence encoding the second AP2 domain and the other in the microRNA172-binding site. The Qs1 allele did not significantly affect the GPC or other processing quality parameters, but it adversely affected the GY by decreasing the thousand kernel weight and grain number per spike. In contrast, Qc1-N8 positively affected the GPC and GY by increasing the thousand kernel weight and grain number per spike, thereby reversing the unfavorable agronomic characteristics resulting from Qc1. Thus, we generated a novel germplasm relevant for wheat breeding. Furthermore, our findings provide new information useful for enhancing cereal crops via non-transgenic approaches.