Group based at Augusta. Her commander at the time was captain Renato d'Elia. From 20 to 27 June 1940 she was deployed to patrol an area north of Mallorca. On June 24, she detected a convoy at long distance, but could not attack. Upon arrival from this mission, she underwent several months of upgrades and repairs. During this time commander D'Elia was replaced by captain Enzo Zanni. In the night between 12 and 13 November 1940 she patrolled in the Gulf of Taranto. From 18 to 21 December 1940 Malachite patrolled northeast of Derna. On December 15, while en route to the area of operations, she was attacked by an aircraft but the attack was beaten back with her anti-aircraft weapons. During the night January 27, 1941 she patrolled in the Strait of Messina. From 9 to 18 February 1941 Malachite patrolled off Bardia. On February 14 she attempted an attack on an unidentified warship, but fails to launch torpedoes due to the high speed of the target. From 15 to 22 March 1941 she was deployed in the Kythira Strait. On the night of March 19, Malachite sighted a cruiser escorted by several destroyers. At 01:19 she launched two torpedoes but they both miss. Malachite was forced to dive and undergo lengthy depth charge attack. From 10 to 18 April 1941 she was posted northeast of the Gulf of Sollum. At 23:37 on April 14 Malachite sighted a large convoy but was prevented from attacking it due to preemptive action by the escorts. On May 20, 1941 Malachite together with numerous other submarines was deployed to an area between Crete, Alexandria and Sollum, to support the German invasion of Crete (Operation Merkur). Malachites area operation was south of the island of Gaidaro. On the night of June 19, 1941 while patrolling off Crete, Malachite sighted a British cruiser escorted by a destroyer. She launched two torpedoes at the target, but they both missed her by the stern. From 3 to 14 July 1941 she patrolled north of Ras Azzaz. At 20:00 on July 3 Malachite sighted a large cruiser (possibly ) escorted by two destroyers, and immediately launched a torpedo. There was an explosion heard, but there is no reports of this attack in British post-war documents, although some believe an escort was hit. From September 25 to October 5, 1941 she patrolled off Ras Aamer. From January 20