Bacterial protein toxins are involved in a number of infectious and foodborne diseases and are considered as potential biological warfare agents as well. Their sensitive multiplex detection in complex environmental, food, and biological samples are an important although challenging task. Solid-phase immunoaffinity capture provides an efficient way to enrich and purify a wide range of proteins from complex mixtures. We have shown that staphylococcal enterotoxins, for example, can be efficiently enriched by means of magnetic immunocapture using antibody functionalized paramagnetic beads. The method was successfully interfaced by the on-beads and off-beads detection using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry at the protein level and by the off-beads nano-electrospray ionization-MS/MS detection at the enzyme digests level, enabling thus the unambiguous identification of the toxin. The method is applicable to any bacterial toxin to which an antibody is available.