Along with land consolidation and the recent increase in the scale of farming in Japan, it is important to assess the relationships between soil properties, topography before land consolidation, and crop characteristics within fields through on-farm research. The objectives of this study were to evaluate the impacts of soil properties and presence/absence of former trenches before land consolidation on winter wheat emergence and yield using non-spatial and spatial linear mixed-effects models, to examine the feasibility of precision agricultural technologies. Results show that the reduction of the seedling establishment ratio may be attributed to high clay content, which was a yield-limiting factor in some cases. Furthermore, locations that were trenches before land consolidation had a 0.92–0.99 t ha−1 lower yield in a drier year. Therefore, the appropriate agronomic practices and implementation of precision agriculture technologies may vary depending on the spatial distribution of soil properties and topography before land consolidation. Our study further showed that a systematic sampling scheme failed to evenly cover the locations of former trenches, which highlighted the importance of stratified sampling based on covariate maps to improve model parameter estimation accuracy.