Nuclear magnetic resonance (NMR) spectroscopy is one of the most promising methods for use in metabolomics studies as it is able to perform non targeted measurement of metabolites in a quantitative and non-destructive way. Sample preparation of liquid samples like urine or blood serum is comparatively easy in NMR metabolomics, because mainly buffer and chemical shift reference substance are added. For solid samples like feces suitable extraction protocols need to be defined as initial step, where the exact protocol depends on sample type and features. Focusing on short chain fatty acids (SCFAs) in mice feces, we describe here a set of extraction protocols developed with the aim to suppress changes in metabolite composition within 24 h after extraction. Feces are obtained from mice fed on either standard rodent diet or high fat diet. The protocols presented in this manuscript are straightforward for application, and successfully minimize residual bacterial and enzymatic activities. Additionally, they are able to minimize the lipid background originating from the high fat diet.