Malessa was born in the Russian Empire to Władysław Izdebski and Maria née Krukowska. After moving back to Poland, she finished a trade school in Łuck in 1924. She worked in the Main Statistical Office in Warsaw and afterward moved to Gdynia. In 1935 she married Wojciech Malessa, but divorced him two years later.
After the Home Army was disbanded in January 1945, Malessa joined the anti-communist resistance organization NIE. After NIE ceased in May 1945, she was a member of the leadership committee of another anti-communist movement, Freedom and Independence. In late 1945, she expressed the desire to leave the organization. While she was in the process of being officially discharged, she was arrested by the Communist secret police who had managed to penetrate the organization's ranks. During the interrogations that followed her arrest, she trusted the "officer's word of honor" given by the UB chief Józef Różański that if she revealed the command and structure of Freedom and Independence, none of the persons she mentioned would be arrested, and further persecution directed at former AK soldiers stopped. With the permission of her commanders, Col. Jan Rzepecki and Col. Antoni Sanojcy who also took Różański's promise in good faith, she gave the UB a list of names of members and commanders of the organization. They were quickly arrested and Malessa, who was still in prison, began a hunger strike as a protest against the breaking of the promises. On 14 February 1947, she was sentenced to two years incarcerations. A few days later, she was "pardoned" by the President of communist Poland, Bolesław Bierut and released. She continued her hunger strike in front of the walls of the Mokotów Prison where those she had named were imprisoned. She immediately began making efforts to have the authorities fulfill the promises they had made and to have the soldiers of the underground released from prison. She wrote letters to Bierut, to the Minister of Security, Stanisław Radkiewicz, and to Różański. Her efforts were unsuccessful; more and more WiN soldiers were arrested and sentenced to long prison terms or death. Shunned by the remains of the anti-communist underground and full of guilt, Emilia Malessa committed suicide on 5 June 1949. She was initially buried at Brodnowski Cemetery in Warsaw. On 19 September 2005, her body was exhumed and after a mass, the urn with her remains was re-buried at the Powązki Military Cemetery.