Isabel acceded to their request. Initially, she was assigned a task to photograph military and strategic sites in Israel and if she is caught she will avoid finding out that she is doing this as part of a covert operation. She successfully passed the tests. 

She was later trained in deciphering aerial photographs and reading topographic maps, using weapons and a Morse device. She was diagnosed as competent for the mission and met with the head of the Mossad, Issar Harel, after he retired Met with his successor in the position of Meir Amit.

In April 1963, Isabel Pedro left for her mission. Her first stop was in Paris where she met Yitzhak Shamir, who was the commander of the unit that operated agents in target countries. 

Shamir trained her for her mission to Egypt which was at that time, under the rule of Gamal Abdel Nasser, the main enemy of the State of Israel, which faced Israel in the 1950s through the sabotage operations of the Fedayeen, and Israel fought against it on the battlefield in the Sinai War, after which the enmity continued to prevail between the two countries. Shamir prepared her for her mission in Egypt and she set off.

Isabel Pardo entered Egypt on a tourist visa with a Uruguayan passport. Since her passport had stamps from the State of Israel, she soiled it and at the Uruguayan consulate in Amsterdam she exchanged it for a new passport which she presented in Egypt. She arrived in Egypt equipped with a Morse device and a radio for receiving shortwave broadcasts. Upon arriving in Egypt she stated that she came to Egypt to study archeology and to practice painting.

At first, Isabel Pardo lived in a luxury hotel where Egyptians from the upper classes were staying. She befriended an archaeologist who traveled throughout Egypt. He agreed to join the young woman who showed an interest in archaeology. Later she met a senior Egyptian journalist close to the Egyptian government. 

He introduced her to a senior military officer who invited her to the sports club in the Zamalek district where she had the opportunity to meet the ladies of high society. One of them used to meet with Isabel at the "Groupy" cafe where senior Egyptian army officers huddled. From all these acquaintances I drew a wealth of intelligence information. In her travels throughout Egypt, she inspected military bases and military airports. 

During her service Pedro managed to obtain the plans for the Aswan Dam which was a strategic objective of utmost importance. The information she collected, including documents and photographs, she sent to Israel, but not directly from Egypt but through acquaintances from Spain who left Egypt and sent the material by mail to Israel, without knowing what was contained in the envelopes. 

In 1965, after three years of mission in Egypt, Isabel asked to return to Israel to start a family. When she returned to Israel, she retired from the Mossad.