Metabolomics studies using a small amount of cells may save time and money, while in some cases (e.g., profiling pathogenic cells in an early-stage tissue), only a small number of cells are accessible for analysis. The analysis of small amounts of biological samples challenges the analytical toolbox used in present-day metabolomics studies, and a significant number of crucial biological questions cannot be properly addressed. To allow metabolic profiling of limited sample amounts, the potential of capillary electrophoresis-mass spectrometry (CE-MS) using a sheathless porous tip interface has been assessed using HepG2 cells in starting amounts of 500 and 10,000 cells as a model system in this work. It is shown that highly efficient and information-rich metabolic profiles for cationic metabolites at low-pH separation conditions could be obtained by sheathless CE-MS using an injection volume of only circa 42 nL, which equals the content/aliquot of circa 0.25 and 5 HepG2 cells, respectively. With as little as the content of 0.25 cell injected, more than 24 cationic metabolites could be identified. A further improvement of sample preparation and/or the injection part is required in order to effectively analyze the compounds of interest in very low sample amounts by sheathless CE-MS. However, the results obtained so far clearly indicate the strong potential of the proposed method for metabolic profiling of limited sample amounts.