Emerging genomic evidence has identified ancestral strains of Yersinia pestis in ancient human populations, sparking debates about its pathogenic role in Neolithic societies. While some researchers attributed Scandinavian Neolithic population decline to plague epidemics, we argue that early Y. pestis strains were more likely associated with outbreaks of benign foodborne enteritis rather than deadly flea-borne plague. This hypothesis is supported by genetic, archaeological, and ecological analyses, which indicate that Y. pestis evolved key flea-borne transmission mechanisms only later in its history.