Production functions to explain regional wheat yields have not been studied extensively in the Canadian prairies. The objective of this study is to employ a Just-Pope production function to examine the relationship between fertilizer inputs, soil quality, biodiversity indicators, cultivars qualifying for Plant Breeders’ Rights (PBR), and climatic conditions on the mean and variance of spring wheat yields. Using regional-level wheat data from Manitoba, Canada, model results show nitrogen fertilizer, temporal diversity, and PBR wheat cultivars are associated with increased yield variance. Mean wheat yield is reduced by the proportion of land in wheat, the interaction of growing temperature and precipitation, and spatial diversity. By contrast, higher soil quality and PBR wheat cultivars increase mean yield. The wheat yield increases attributed to PBR range from 37.2 (1.4%) to 54.5 kg/ha (2.0%). Plant Breeders’ Rights may have enhanced royalties from increased certified seed sales, but the benefits in terms of higher wheat yield or lower yield variability are limited. Future research is required to understand the interactive effects of fertilization practices, genetic diversity, and environmental conditions on regional wheat yield stability.