Foodborne diseases caused by bacteria and their endotoxins and exotoxins hold enormous relevance for the public health sector, in particular in the context of the ever-growing globalization where proper monitoring and risk management approaches are still missing. Therefore, detection of bacteria and their exotoxins in food has been increasingly tackled by novel approaches and methods known as “-omics” methods. Bacterial genome sequencing proved to be the most mature technological platform for routine surveillance of microbiological risk assessment, while proteomics tools are increasingly used for fast bacterial subspecies differentiation, analysis of protein secretome, or as alternatives to immunoassay. In particular, mass spectrometry-based techniques showed a superior performance in descriptive and quantitative applications and methods combining liquid chromatography to mass spectrometry (LC-MS and LC-MS/MS) are constantly developed for increased proteome coverage. Still, initial high investments in mass spectrometry instrumentation and open issues in protocol optimization seems to be major bottlenecks for broader use of this technique in routine food analyses.