Bacillus cereus sensu lato is frequently involved in foodborne toxico-infections and is found in various foodstuff. It is unclear whether certain strains have a higher affinity for specific food matrices, which can be of interest for risk assessment. This study reports the characterization by whole-genome sequencing of 169 B. cereus isolates, isolated from 12 food types and soil over two decades. Any potential links between the food matrix of isolation, the isolate's genetic lineage and/or their (putative) virulence gene reservoir were investigated. More than 20 % of the strains contained the genes for the main potential enterotoxins (nheABC, hblCDA and cytK_2). Cereulide biosynthesis genes and genes encoding hemolysins and phospholipases, were detected in multiple isolates. Strain typing revealed a high diversity, as illustrated by 84 distinct sequence types, including 26 not previously described. This diversity was also reflected in the detection of all seven panC types and 71 unique virulence gene profiles. Core-genome MLST was used for phylogenomic investigation of the entire collection and SNP-based clustering was performed on the four most abundant sequence types, which did not reveal a clear affinity for specific B. cereus lineages or (putative) virulence genes for certain food matrices. Additionally, minimal genetic overlap was observed between soil and foodborne isolates. Clusters of closely-related isolates with common epidemiological metadata were detected. However, some isolates from different food matrices or collected several years apart were found to be genetically identical. This study provides elements that can be used for risk assessment of B. cereus in food.