No. 3 Squadron's longest-serving commanding officer (CO) during the war was Squadron Leader Bobby Gibbes, whose tour lasted from February 1942 to April 1943. Gibbes was replaced by Squadron Leader Brian Eaton, who led the unit until February 1944. During this period, No. 3 Squadron took part in the Allied invasions of Sicily and Italy. It re-equipped with P-51 Mustangs in November 1944 and continued to operate in Italy and Yugoslavia until the end of the European war in May 1945. No. 3 Squadron's record of 25,663 operational flight hours and 217.5 enemy aircraft destroyed made it the highest-scoring RAAF fighter squadron.