The importance of animal welfare and organic production of chicken eggs has increased in the European Union in recent years. Legal regulation for organic husbandry makes the production of organic chicken eggs more expensive compared to conventional husbandry and increases the risk for food fraud. Therefore, the aim of this study was therefore to develop a non-targeted LC-ESI-IM-qToF-MS method based on 270 egg samples that achieved a classification accuracy of 96.3%. Subsequently, Surrogate Minimal Depth (SMD) was applied to select important variables identified as carotenoids and lipids based on their MS/MS spectra. LC-MS results were compared with FT-NIR spectroscopy analysis as a low-resolution screening method and achieved 80.0% accuracy. Here, SMD selected parts of the spectrum which are associated with lipids and proteins. Furthermore, we used SMD for a low-level data fusion to analyze relations between the variables of the LC-MS and the FT-NIR spectroscopy datasets. Thereby, lipid-associated bands of the FT-NIR spectrum were related to the identified lipids from LC-MS analysis, demonstrating that FT-NIR spectroscopy partially provides similar information about the lipidome. In future applications, eggs can therefore be analyzed with FT-NIR spectroscopy to identify conspicuous samples that can subsequently be counter-tested by mass spectrometry.