At the outbreak of World War II, Margottini was the commanding officer of the 11th Destroyer Squadron, with flag on the destroyer "Artigliere". On 9 July 1940 he participated in the Battle of Calabria, where he led his Squadron in a gun and torpedo attack on the British fleet, receiving for this action the Bronze Medal of Military Valor. In the following months he carried out several missions from Messina and Augusta. On 11 October 1940, he took to the sea with the ships of his squadron to carry out a night search for a British naval force reported in the Sicilian Channel, in cooperation with ships of the 1st Torpedo Boat Squadron.