The reformulation of dairy products with plant ingredients poses new food safety challenges, particularly microbiological risks. Due to their proximity to the soil, plant ingredients are susceptible to contamination with spore-forming bacteria such as Bacillus spp., with toxin-producing Bacillus cereus posing a health risk. Here, we examined the contamination of a plant-based raw material used for a cheese alternative with B. cereus at various stages of the production process and how it can be inhibited by fermentation. The raw material consisted of a paste containing 40% shelled sunflower seed oil press cake. The concentration of B. cereus in the untreated paste was below the quantification limit of 50 CFU/g vegetative cells or spores. However, after heat treatment and incubation at room temperature, the vegetative cell counts increased to potentially toxin-forming concentrations of >105 CFU/g within 22 h if no simultaneous fermentation with lactic acid bacteria took place. Simultaneous mesophilic fermentation to a final pH of 4.9 reproducibly inhibited the growth of B. cereus but not at a final pH of 5.7. During the subsequent one- and two-month storage at 4 °C, the B. cereus numbers in all fermented masses dropped sharply to <200 CFU/g, despite previous potentially toxigenic B. cereus levels of >105 CFU/g. The decrease in vegetative cells was not associated with a corresponding increase in spores. Based on these findings, we recommend monitoring B. cereus in new dairy alternatives both after heat treatment and immediately following the end of fermentation to support the development of a safe production process.