The abuse and incorrect administration of antibiotics has resulted in an increased proliferation of bacteria that exhibit drug resistance. The emergence of resistant bacteria has become one of the biggest health concerns globally, and an enormous effort has been made to combat them. However, despite the efforts, the emergence of resistant strains is rapidly increasing, while the discovery of new classes of antibiotics has lagged. For this reason, it is pivotal to acquire a more detailed knowledge of bacterial resistance mechanisms and the mechanism of action of substances with antibacterial effects to identify biomarkers, therapeutic targets, and the development of new antibiotics. Metabolomics and proteomics, combined with mass spectrometry for data acquisition, are suitable techniques and have already been applied successfully. This review presents basic aspects of the metabolomic and proteomic approaches and their application for the elucidation of bacterial resistance mechanisms.