In the absence of established best practice standards in the probiotic field for reducing the risk of bacterial transfer between experimental groups, we developed protocols and methods to ensure the highest quality and interpretability of results from animal studies, even when performed in non-conventional animal care facilities. We describe easily implementable methods for reducing cross-contamination during animal housing, behavioural testing, and euthanasia, along with highlighting protocols for contamination detection in experimental subjects and laboratory areas using qPCR. In light of the high cross-contamination risks between animals during experiments involving probiotics, constant vigilance in animal care and research protocols is critical to ensure valid and reliable research findings.