We investigated an atypical Listeria monocytogenes strain isolated from the food processing environment, which may evade widely used diagnostic approaches. After species confirmation using PCR and MALDI-TOF, enzyme analysis revealed reduced phospholipase activity, indicating a link between its activity and the white appearance of atypical strains on chromogenic agar. While no mutation was detected in the phospholipase C gene, comparative genomics revealed a distinct seven base pair insertion in the prfA gene, resulting in gene truncation. These results highlight the risk of false negatives in current diagnostics and a need for improved detection methods to ensure food safety.