After her father's death, Lily returned to Kuching with her mother and continued her study until Standard Seven (equivalent to Form Three, age 15) at St. Mary's Mission School.
Having had a European lifestyle in Singapore, when she returned to Kuching she missed her previous freedom and found it difficult to start covering her head and be confined to the house.
Her knowledge about her new religion impressed her neighbours, to the extent that many people in the village sent their sons to Lily to learn to read the Quran.
This gesture showed that the people in the village trusted her and respected her highly as women were rarely consulted for religious teaching in that era.
In 1929, she resigned from this post when the Brooke Government appointed her as the Principal of the Permaisuri Malay Girls’ School, which was opened in Kuching in 1930.
In March 1947, she was elected as the chairperson of the women's wing of the Malay National Union of Sarawak(PKMS), a leading group in the Anti-Cession Movement.
In an interview by The Straits Times Singapore dated 21 July 1947 on the Anti-Cession movement, Lily Eberwein expressed her concern for its impact on Malay education.
She emphasised that the position of education in Sarawak must remain a matter of gravest public concern “for as long as this unhappy controversy lasts”, referring to cession.
She also stated, “We Malays, in conjunction with the other indigenous races, will fight with unwavering purpose for the redress of the wrong that has been done to our people in the extinction of our nationhood and independence”.
This met with considerable support from women of all ages from throughout the count.” Although Lily Eberwein was a very active anti-cessionist, she never joined any political parties.
She participated actively in various voluntary organisations such as the Prisoners’ Aid Society, Anti-Tuberculosis Association Sarawak (ATAS), and the Red Cross.