As a special field agent for the Agricultural Adjustment Administration (AAA) in the 1930s and 40s, she worked to improve the lives of rural African Americans in the South.

As the principal's wife, Jennie Moton devoted much of her time to the Institute; historian Janet Sims-Wood calls her "the driving force behind her husband."

[4] In 1920, Moton was one of the speakers at a conference of the Commission on Interracial Cooperation in Memphis, Tennessee, along with Washington, Elizabeth Ross Haynes, and Charlotte Hawkins Brown.

Addressing a white audience, the women offered their perspective on topics such as child welfare, suffrage, education, protection of Black girls, and the eradication of lynching.

In 1941, Moton, Bethune, and A. Philip Randolph helped persuade Roosevelt to sign Executive Order 8802, which prohibited discrimination in the defense industries based on "race, creed, color or national origin."

Moton's special task was "to contact Negro farm women in the Southern region in order to get their viewpoint" on the program as well as providing them with information.

During her final years she served as a member of the Margaret Murray Washington Memorial Foundation, and in 1942 was appointed a home nursing consultant for the National Red Cross.