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In 1982, Lundy became the director of the National Student Young Women's Christian Association in New York. There, she established a regional coalition on sanctuary and co-chaired the Sanctuary Committee at Riverside Church. In 1986, she assisted in transporting a refugee family from Tucson, Arizona, to Riverside Church.
That same year, during the trial of Presbyterian minister John Fife and other sanctuary movement leaders, Lundy and 11 fellow activists were called to testify. She refused and was placed under house arrest for the trial's duration.
In 1987, Lundy became the director of the Women's Ministry Unit of the Presbyterian Church (USA), later renamed Women's Ministries in 1994.
She co-chaired the US committee for the WCC ecumenical decade Churches in Solidarity with Women (1988–1998). As part of this initiative, she helped organize the 1993 Re-Imagining Conference in Minneapolis, which gathered over 2,000 participants worldwide to explore feminist theology and rituals. The conference faced criticism for its use of the term "Sophia" in prayers, leading to accusations of heresy and witchcraft. Despite the General Assembly Council's initial decision to take no action, Lundy was removed from her position in May 1994.
“I was looking for a woman to fill the position of deputy general secretary which had become vacant after Mercy Oduyoyes’ departure in 1994,” recalled Rev. Dr Konrad Raiser, former WCC general secretary. “I received strong recommendations to consider Mary Ann whom I had not yet met.”
Lundy served as WCC deputy general secretary from 1995-1999.
“Her responsibility was essentially to oversee and coordinate the programmatic activity of the council in four newly formed units,” said Raiser. “Because of her seniority and her broad experience she quickly gained the acceptance and trust of the four directors and their colleagues. With her warm and generous personality she strengthened the leadership team of the council and we developed a trusted relationship.”
In the run-up to the WCC 8th Assembly in Harare, she was responsible for organizing the first ever systematic process of programme evaluation. “The evaluation showed that all four units and the newly appointed commissions had developed a clear programmatic profile,” recalled Raiser. “However, it also became evident that the hope for a clearer programmatric integration through the new structure had not fully materialized.”
Shortly after the WCC 8th Assembly, in early 1999, Lundy left retired. “I preserve a very warm and grateful memory of the time of our working together in the general secretariat,” said Raiser.
