In 1960, the French government drafted Huston’s husband, Dr. Yves Champey, and the army appointed him physician in charge of a large segment of the population in Aïn Mokra, in the most dangerous Algerian region of the Constantinois. Accompanied by Huston and their daughter Françoise, he supported French troops who were fighting against the warriors for independence, and with Huston’s support he also provided illegal medical care to the fellagha, considered terrorists by the French, and called "Algerian freedom fighters" by the English-speaking press.
Meanwhile, Huston was pregnant with their second child. Not wanting the baby to be born into a war-torn country, Huston crossed the border into Tunisia with Françoise. There her second daughter, Jeanne Marie, was born on June 24, 1961. Huston stayed in Tunisia after her birth and worked for the Tunisian Ministries of Information and Foreign Affairs, assisting as secretary, translator, and English communications officer until the French-Algerian War ended in 1962.
While in Algeria, Huston began her life-long advocacy for people living in developing countries, especially rural women. After the country’s 1962 independence, Huston and Champey returned to Algeria to assist in setting up a comprehensive public health care system. Perdita became a medical social worker, distributing food, helping to deliver babies and writing for the illiterate. Additionally, Huston was a research assistant for The New Yorker (1963), consular foreign affairs officer for the UN in Algiers, and a freelance writer (1963-66).