Abstract Among all the “-omics” studies, metabolomics currently has the most growth potential. The complexity of the studied matrices demands from the analytical chemist the development of new protocols and the modification of existing methods to obtain a full biochemical image of the sample. In the current review, we discuss the advantages and the disadvantages of solid-phase microextraction based on up-to-date metabolomics studies performed on plants, biofluids, tissues and cell cultures. We place particular emphasis on the development of new extraction phases in view of the analyte coverage and on the features of the method, which complement solvent-based extraction technologies.