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Background: In Italy an autogenous registered vaccine, adjuvanted with aluminum hydroxide, can be administrated to contrast Salmonella enterica subsp. enterica serovar Abortusequi infection, coupled to a specific antimicrobic treatment. Case Description: Here, we report the case of an abortion outbreak by Salmonella Abortusequi in Central Italy, where mares were vaccinated but immediately developed a strong local reaction, maybe due to the adjuvant. Promptly, another autogenous vaccine, substituting the aluminum hydroxide with a new generation adjuvant (Montanide™ Seppic IMS 1313), was produced and administrated. The new formulated vaccine did not cause any adverse outcome and conferred high protection titers against the infection. As far as we know, this is the first reported case of immunization by a vaccine adjuvanted with Montanide™ Seppic IMS 1313 in horses. Conclusion: This approach may be used as a preventive strategy for further outbreaks in association with the application of recommended biosafety principles.