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<i>Shigella</i> spp. and <i>E. coli</i> are closely related and cannot be distinguished using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) with commercially available databases. Here, three alternative approaches using MALDI-TOF MS to identify and distinguish <i>Shigella</i> spp., <i>E. coli</i>, and its pathotype EIEC were explored and evaluated using spectra of 456 <i>Shigella</i> spp., 42 <i>E. coli</i>, and 61 EIEC isolates. Identification with a custom-made database resulted in >94% <i>Shigella</i> identified at the genus level and >91% <i>S. sonnei</i> and <i>S. flexneri</i> at the species level, but the distinction of <i>S. dysenteriae</i>, <i>S. boydii</i>, and <i>E. coli</i> was poor. With biomarker assignment, 98% <i>S. sonnei</i> isolates were correctly identified, although specificity was low. Discriminating markers for <i>S. dysenteriae</i>, <i>S. boydii</i>, and <i>E. coli</i> were not assigned at all. Classification models using machine learning correctly identified <i>Shigella</i> in 96% of isolates, but most <i>E. coli</i> isolates were also assigned to <i>Shigella</i>. None of the proposed alternative approaches were suitable for clinical diagnostics for identifying <i>Shigella</i> spp., <i>E. coli</i>, and EIEC, reflecting their relatedness and taxonomical classification. We suggest the use of MALDI-TOF MS for the identification of the <i>Shigella</i> spp./<i>E. coli</i> complex, but other tests should be used for distinction.