Bacillus cereus is an important food-borne pathogen and spoilage organism. In this study, numerous phenotypes and the genomes of B. cereus strains ATCC 14579 and ATCC 10987 were analysed to compare their metabolic capacity and stress resistance potential. The growth performance of the two strains was assessed for nearly 2000 phenotypes, including use of nutrient sources, performance in acid and basic environments, osmo-tolerance and antibiotic resistance. Several food-relevant phenotypic differences were found between ATCC 14579 and ATCC 10987, such as differences in utilization of carbohydrates, peptides, amino acids and ammonia. Subsequently, the genomes of both strains were analysed with INPARANOID to search for strain-specific open reading frames (ORFs). B. cereus ATCC 14579 and ATCC 10987 were found to harbour 983 and 1360 strain-specific ORFs respectively. The strain-specific phenotypic features were interlinked with corresponding genetic features and for several phenotypic differences a related strain-specific genetic feature could be identified. In conclusion, the combination of phenotypic data with strain-specific genomic differences has led to detailed insight into the performance of the two B. cereus strains, and may supply indicators for the performance of these bacteria in different environments and ecological niches.