In the same year, Perla carried out an extensive training cruise that took her to Tobruk, Benghazi, Bardia, Leros, Rhodes, and other ports in the Dodecanese eventually returning to Augusta.

The results were disappointing: it was discovered that stormy sea prevented the use of submarine's armament and made it very difficult even to remain at a periscope depth.

[6] At the time of Italy's entrance into World War II Perla was again in Massawa as part of 82nd Squadron and commanded by captain Mario Pouchain.

[2] According to the initial orders, Perla was supposed to remain in Massawa during the first weeks of the war, but Viceroy Amedeo de Aosta demanded that two additional submarines be deployed in the operations area.

Perla left Massawa on the afternoon of 19 June 1940 to patrol an area in the Gulf of Tadjoura about 15 nautical miles from Ras-El Bir.

The captain ordered inspection and maintenance to be conducted, and the submarine surfaced during the night of 21 June to minimize the risk of poisoning.

At dawn, Perla submerged and soon after several crew members fell ill. As time went by, more men became ill, and the ones already suffering started exhibiting signs of chloromethane poisoning, including hallucinations.

The submarine was forced to crash dive and stay at the bottom for a few hours while depth charges were launched by the enemy, but sustained minimal damage.

On the evening of 26 June Perla again surfaced and continued her trip back to Massawa; however, during the night, when she was about 20 miles from Sciab Sciach lighthouse, she ran aground.

[2] A message was sent to Massawa, requesting help, and the destroyers Leone and Pantera together with torpedo boat Giovanni Acerbi were dispatched.

Only the timely arrival of two Italian air groups (eight SM-81 bombers) saved Perla as they attacked the enemy ships and forced them to flee.

[7][2] On 15 July a rescue ship arrived from Massawa, and in five days Perla was hastily repaired to bring her into sailable condition.

In January 1941, when it became clear that Italian East Africa would eventually fall, it was decided to send submarines to Bordeaux to try to save them from either destruction or capture by the British.

Perla as well as other submarines were modified for the journey: her fuel tanks were enlarged, some torpedoes, gun ammunition were removed as well as some non-critical items.

[8] Atlantis' skipper, Bernhard Rogge, wrote in his memoirs that, after seeing the small coastal submarine and its emaciated crew, he told the commander, Lt. Bruno Napp, his perplexity about his mission and suggested to him to reach either Brazil or Argentina to be interned; by his account, Napp politely rejected the advice, telling that he would do his utmost to obey his orders, much to Rogge's admiration.

On 10 May she was deployed to patrol off Kelibia along the Tunisian coast and on the following day Perla sighted HMS Welshman east of the island of La Galite and launched two torpedoes at the target, but they both missed.