An evaluation of the efficacy of 35% hydrogen peroxide vapour (HPV) against two strains of FMDV was conducted over a period of 6 months. FMDV biological indicators were produced on‐site using strains obtained from a commercial FMDV vaccine manufacturing process. FMDV biological indicators were distributed within a BSL4 laboratory and exposed to short duration hydrogen peroxide cycles. Variations in titre, support matrix (soiling), temperature and humidity were evaluated in a series of 16 exposures using over 200 individual FMDV indicators. Additional verification testing was performed in an operational material transfer lock to replicate real‐world use. HPV was found to be efficacious in inactivating FMDV strains; the inoculum titre influenced the level of reduction achieved with the specified cycle. Significance and Impact of the Study The classification of formaldehyde as a presumed human carcinogen has presented regulatory challenges for its continued use as a biocidal product. Institutions are actively seeking fumigants to replace formaldehyde and undertaking studies to validate biocidal efficacy, particularly in high‐level biosafety facilities where the consequences of pathogen release can be extremely severe. This study builds on the already substantial scientific efficacy base of 35% hydrogen peroxide vapour and provides a comprehensive evaluation of the applicability of hydrogen peroxide vapour as a replacement for formaldehyde within a Foot & Mouth Disease (FMDV) vaccine manufacturing facility. Significance and Impact of the Study: The classification of formaldehyde as a presumed human carcinogen has presented regulatory challenges for its continued use as a biocidal product. Institutions are actively seeking fumigants to replace formaldehyde and undertaking studies to validate biocidal efficacy, particularly in high‐level biosafety facilities where the consequences of pathogen release can be extremely severe. This study builds on the already substantial scientific efficacy base of 35% hydrogen peroxide vapour and provides a comprehensive evaluation of the applicability of hydrogen peroxide vapour as a replacement for formaldehyde within a Foot & Mouth Disease (FMDV) vaccine manufacturing facility.