Chia seeds are becoming more and more popular in modern diets. In this contribution NIR and 2D-fluorescence spectroscopy were used to determine their nutritional values, mainly fat and protein content. 25 samples of chia seeds were analysed, whereof 9 samples were obtained from different regions in Kenya, 16 samples were purchased in stores in Germany and originated mostly from South America. For the purchased samples the nutritional information of the package was taken in addition to the values obtained for fat and protein, which were determined at the Hohenheim Core Facility. For the first time the NIR and fluorescence spectroscopy were used for the analysis of chia. For the spectral evaluation two different pre-processing methods were tested. Baseline correction with subsequent mean-centring lead to the best results for NIR spectra whereas SNV (standard normal variate transformation) was sufficient for the evaluation of fluorescence spectra. When combining NIR and fluorescence spectra, the fluorescence spectra were also multiplied with a factor to adjust the intensity levels. The best prediction results for the evaluation of the combined spectra were obtained for Kenyan samples with prediction errors below 0.2 g/100 g. For all other samples the absolute prediction error was 0.51 g/100 g for fat and 0.62 g/100 g for protein. It is possible to determine the amount of protein and fat of chia seeds by fluorescence and NIR spectroscopy. The combination of both methods is beneficial for the predictions. Chia seeds from Kenya had similar protein and lipid contents as South American seeds.