Spices and herbs are potential vectors for virulent and pathogenic micro-organisms, which cause illness in consumers, contribute to spoilage, and reduce the durability of foodstuffs. The present study aims to provide relevant data about virulence and antibiotic resistance of Bacillus cereus isolated from various spices. A total of 200 samples of 8 types of spices (black pepper, chilli, white pepper, cumin, cinnamon, turmeric, curry powder, and sumac) were collected from various markets, retail shops, and sucuk production premises located in the Isfahan province of Iran. Presumptive B. cereus strains were obtained using Bacara Agar plates after enrichment in saline peptone water and final colonies were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Enterotoxin (HBL) and nonhaemolytic enterotoxin (NHE) production were assessed using the Duopath® Cereus Enterotoxins Test kit. The Kirby–Bauer disc diffusion method was applied as antibiotics susceptibility test. PCR was used to detect Emetic toxin gene (CES and CER) and enterotoxigenic toxin gene (cytK, nheA, hblC, and entFM). Results show a significant prevalence of B. cereus (42%) in spices. However, the spices meet food safety recommendations (<104 cfu/g). Antibiotics susceptibility test show alarming rate of resistance to beta-lactam antibiotics specially ampicillin (83.33%) and penicillin (82.14%). Concerning the toxin producing capacity more than half of the isolates (51.19%) produce NHE toxin and 27.38% produce HBL toxin. The most abundant gene were nheA, nheB, and nheC and a combination of 4 genes (entFM, nheA, hblC, and cytK) was detected in many isolates. In conclusion, the presence of multidrug resistant B. cereus strains carrying diarrhoeal toxin-encoding genes in spices intended for human consumption represents a serious health hazard. These results indicate the need for regular surveillance of the occurrence of B. cereus strains in spices and food products in Iran.