Agriculture, especially meat and milk production, is responsible for a large part of the annual surplus in the nitrogen balance worldwide. The efficient use of ingested protein, i.e., its conversion into milk protein, is of great importance for a sustainable dairy production. Unused protein is excreted in the form of nitrogen compounds. These compounds are known to have detrimental effects on the environment, including soil degradation and eutrophication of water bodies. Additionally, when manure is applied to arable land, nitrous oxide can be formed, which has an even higher global warming potential than methane. Previous studies have shown phenotypic and genetic differences in nitrogen use efficiency (NUE); however, to date, there is no evidence that genetic correlations exist between NUE and methane emissions, and thus, whether trade-offs or opportunities for indirect selection are to be expected. The aim of this study, which started in January 2022, is to determine the genomic variation in NUE and methane emissions in dairy cows in Switzerland. The data collection will extend over a period of four years, including dairy cows from the experimental farm at Agroscope in Posieux, cantonal and private farms. The cows sampled in this study are fed with herbage (grazed or not), hay, grass silage, maize silage and/or concentrates depending on the farm conditions and the season. Samples from cows between day 90 and day 250 of lactation are collected directly at the farms in close cooperation with the farmers. The reference method for phenotyping NUE and methane emissions is laborious and costly. It requires specialised equipment, such as weighing troughs with individual cow identification to record feed intake and the GreenFeed® system, which measures with high precision the methane output via the cow's breath. Therefore, to allow for higher throughput, we will employ prediction models developed with near- (NIR) and mid-infrared spectroscopy (MIR). NIR spectra of freeze-dried milk and faeces, and MIR spectra of fresh milk will be used to estimate NUE and methane emissions. With the continuous collection of NUE and methane emissions reference data, we aim to constantly improve the accuracy of predictions and contribute to international consortia. After one year, milk, faeces and hair samples from more than 400 cows were collected, and we genotyped these cows via low-pass sequencing. We will conduct a genome-wide association study to gain detailed knowledge about the gene variants associated with variation in NUE and other relevant traits, such as residual nitrogen intake in dairy cows. The knowledge generated in this study could improve the selection strategies to increase NUE and decrease methane emissions of dairy cattle, and simultaneously support to reduce protein requirements as well as emissions and losses in animal production in the long term.