In January 2006, Floccari's form was rewarded when Serie A strugglers Messina signed him (jointly-signed with Atalanta from Rimini) as they looked to avoid relegation. Floccari scored three times as Messina survived thanks to the Calciopoli scandal. Two of those goals came in a 2–2 draw with Juventus. In June 2006, Messina bought the remain rights from Atalanta. In his first full season of Serie A in 2006–07, Floccari scored only twice as Messina finished last.