The dataset contains yield and grain protein content data for varieties of winter wheat (Triticum aestivum L.) grown at different locations in Switzerland in the period 1990-2023. The dataset also includes weather data for the respective locations and years, and SNP (single nucleotide polymorphism) marker data for the respective varieties. The varieties and locations have been anonymized using a code. The dataset has been used to develop yield and protein content prediction models. The grain yield and protein content data were collected in the frame of official Swiss winter wheat variety trials that test the varieties for their value for cultivation and use (VCU). The dataset published here is for low input conditions, whereas other conditions such as high input and organic are not included. The multi-environment trials were conducted by AGROSCOPE, the Swiss center of excellence for agricultural research, and took place across the Swiss wheat production zone (from Western to Eastern Switzerland, between 390 and 640 m.a.s.l.) (Herrera et al., 2020). A total of 16 variety trial locations are included in the dataset, with each location being present in 1-34 trial years. The dataset contains yield and protein content data for 98 winter wheat varieties, which are of both Swiss and foreign origin. Each variety was grown in 1-22 years at 8-16 locations. Reference: Herrera J.M., Levy Häner L., Mascher F., Hiltbrunner J., Fossati D., Brabant C., Charles R. & Pellet D., 2020. Lessons From 20 Years of Studies of Wheat Genotypes in Multiple Environments and Under Contrasting Production Systems. Frontiers in Plant Science, 10: 1745. doi.org/10.3389/fpls.2019.01745.