Understanding the inheritance of traits is critical for developing sustainable and environmentally friendly plant breeding programs. Six wheat genotypes, viz., Galaxy-13, Inqilab-91, Ghaznavi-98, Khaista-17, Benazir-13, and Parula, were crossed using a Griffing’s half-diallel scheme, producing 15 F₁ hybrids. These hybrids and their parental lines were assessed using a randomized complete block design with three replications at Cereal Crops Research Institute (CCRI), Pirsabak, and The University of Agriculture, Peshawar (UAP), during 2016-17. The same pattern was observed in F2 population studies conducted in 2017-18. Significant genotype and genotype × environment interaction effects were observed for all traits. The F₁ hybrids generally outperformed their parental lines, highlighting the potential for superior hybrid performance. This study aimed to investigate the genetic mechanisms underlying yellow rust resistance, flag leaf area, 1000-grain weight, and grain yield per plant using Griffing’s combining ability analysis. Analysis revealed that combining ability effects were significant for all traits. Maximum and significant GCA effects were observed in parental cultivars, i.e., Benazir-13 at CCRI, followed by Inqilab-91 at UAP and Inqilab-91 for 1000-grain weight and grain yield per plant at the CCRI and UAP, respectively. However, in the case of SCA effects, the F₁ hybrids Inqilab-91× Galaxy revealed significant SCA effects for grain yield per plant at CCRI and UAP, suggesting nonadditive gene action. These promising populations hold potential for further improvement in yellow rust resistance and grain yield in future breeding efforts. Furthermore, these findings underscore the potential of hybridization in reducing reliance on fungicides by developing yellow rust-resistant varieties. Such environmentally friendly approaches not only minimize chemical inputs but also offer cost-effective and sustainable solutions for wheat production, contributing to ecological conservation and economic benefits for farmers.