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Background Probiotic food supplements (FS) containing live bacteria cultures are widespread in Switzerland. The aim of the study conducted in 2024 was to evaluate the microbiological safety of these products and to review compliance with the legal requirements in accordance with the Ordinance on Food Supplements (VNem, SR 817.022.14). The analysis looked at twenty products, mostly manufactured in the EU, containing three to sixteen probiotic bacteria strains, and in some cases combined with herbal ingredients, minerals or vitamins. The products underwent microbiological testing (microbial count as per ISO 15214) and molecular testing (sequencing using Oxford Nanopore Technology). In the majority of samples (n = 11), all requirements were met, while nine products were flagged as non‐compliant. The main reasons for non‐compliance were insufficient microbial counts per daily dose, discrepancies between the declared and actual bacterial composition, and various labelling deficiencies. No harmful microorganisms or transferable antimicrobial resistance genes (ARG) were detected. Detected ARGs (including aac(6’)‐Ii, msr(C) and tet(W)) are chromosomally coded and currently considered not horizontally transferable. However, products containing Enterococcus (E.) faecium or herbal ingredients (e.g. Chlorella powder) require special attention, as undesirable microorganisms or ARGs could potentially be introduced here. Non‐compliant products were issued with conditions by the competent enforcement authorities, including having to present production documents, investigate causes, adapt their self‐regulation systems and rectify labelling deficiencies. In three cases, sales bans were issued. The study also highlighted the potential of modern sequencing technologies for effective microbiological testing of the bacterial composition of probiotic food supplements. As recommendations, manufacturers and distributors must systematically check and document microbiological quality; mixtures containing E. faecium or herbal ingredients should be specifically tested for contaminants and ARGs; the combination of classical and molecular methods should be established as standard and the testing campaign should be repeated to check the long‐term implementation of the self‐regulation requirement. In conclusion, the tested probiotic food supplements are predominantly safe. The cases of non‐compliance mainly affected quality management and declarations rather than product safety in the stricter sense. However, systematic self‐regulation and improved product monitoring are key to ensuring microbiological quality and consumer safety.