Bekasam is a traditional Indonesian spontaneously fermented fish product whose microbial community has been characterised almost exclusively through culture-based methods that overlook non-culturable and viable but non-culturable organisms. This study applied a metaproteomic approach to profile the microbial community of bekasam and to assess its probiotic potential at the level of expressed proteins. Proteins were extracted from bekasam collected from South Sumatra and analysed by LC-HRMS. Peptides identified with SearchGUI and PeptideShaker were annotated taxonomically and functionally using Unipept. Taxonomic classification was achieved for 19,125 peptides, revealing a mixed community co-dominated by fungi (largely Ascomycota, including Saccharomycetes) and bacteria (largely Pseudomonadota and Bacillota). Functional annotation recovered 6,830 distinct GO terms and 1,388 EC-annotated enzymes; binding activities together with transferases and hydrolases dominated both the GO Molecular Function and EC profiles, while abundant proteolysis and fatty-acid biosynthesis among biological processes were consistent with the amino acid driven flavour development and acidification characteristic of fermented fish. Of 357 peptides assigned to 17 lactic acid bacteria (LAB) genera, species-level resolution showed that 64% of species-resolved peptides belonged to recognised probiotic or fermentation organisms—including Lactiplantibacillus plantarum, Pediococcus pentosaceus, Lactococcus lactis, Lactobacillus acidophilus and four Bifidobacterium species—whereas the apparent genus-level dominance of Streptococcus resolved almost entirely into non-probiotic species. The approach, including species-level resolution of mixed LAB genera, offers a useful framework for assessing the probiotic potential of fermented fish products.

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