Morgan remained associated with Berkeley for more than 50 years, and though she retired in 1954, she was active in her field until just before her death. She received the Garvan Medal from the American Chemical Society and the Borden Research Award from the Borden Company Foundation. At Berkeley, the campus nutrition laboratory is named in her honor. Iota Sigma Pi, an American chemistry honor society, presents the Agnes Fay Morgan Research Award to outstanding women in the field.
