Bacillus cereus is a ubiquitous endospore‐forming bacterium, which mainly affects humans as a food‐borne pathogen. B. cereus can contaminate groundwater used to irrigate food crops. Here, we examined the ability of the emetic strain B. cereus F4810/72 to survive abiotic conditions encountered in groundwater. Our results showed that vegetative B. cereus cells rapidly evolved in a mixed population composed of endospores and asporogenic variants bearing spo0A mutations. One asporogenic variant, VAR‐F48, was isolated and characterized. VAR‐F48 can survive in sterilized groundwater over a long period in a vegetative form, and has a competitive advantage compared to its parental strain. Proteomics analysis allowed us to quantify changes to cellular and exoproteins after 24 and 72 h incubation in groundwater, for VAR‐F48 compared to its parental strain. The results revealed a significant rerouting of the metabolism in the absence of Spo0A. We concluded that VAR‐F48 maximizes its energy use to deal with oligotrophy, and the emergence of spo0A‐mutated variants may contribute to the persistence of emetic B. cereus in natural oligotrophic environments.