Metabolic fingerprints are novel measurement tools to evaluate the biochemical status of a living organism by using 1H NMR and multivariate data analysis (MVDA). In this way, a quick evaluation of changes in health or diseased state can be made, reflected in alterations of metabolic patterns. Normally, metabolic fingerprinting is based on in vivo studies. These studies often represent a labor-intensive and expensive manner of investigation. In vitro studies are not hampered by these disadvantages, thus constituting an interesting alternative. In this research, results are presented of a pilot experiment in which metabolic fingerprinting was combined with an in vitro model. For this purpose, differentiated Caco-2 cells were exposed to inulin and its fermentative metabolites, both dissolved in culture medium. Cells were incubated for 0 or 48 h. Cell fractions were analyzed by NMR, then subsequently with MVDA. Differences in treatment provided detectable variations in the time of metabolic patterns of cell contents. Results indicated that glucose metabolism linked to glutamate was of major importance in the effects of inulin and its metabolites on Caco-2 cells under the conditions of our study. Metabolic fingerprinting in combination with an in vitro model appears to be a feasible technique with which to visualize metabolic patterns of cell contents and provides an efficient place for the generation of hypotheses about the metabolic pathways involved. In vitro metabolic fingerprinting may be of great benefit in the future for a better understanding of the relationship between nutrition and health.