She married John M. Harbert, the founder of Harbert Corporation, whom she had met in grade school. They had two sons, John Murdoch Harbert IV (born with William's Syndrome) and Raymond J. Harbert (who founded Harbert Management Corporation in 1993), and a daughter, Marguerite Harbert Gray. They resided in Mountain Brook, Alabama, and summered in Highlands, North Carolina. They attended St. Mary's on-the-Highlands Episcopal Church.
Her husband predeceased her in 1995. Upon his death, she inherited his fortune. By 2013, she was the wealthiest person in Alabama, with an estimated wealth of US$1.5 billion. She admitted she found it "hard in a way" to be rich.
She served on the Board of Trustees of her alma mater, Birmingham-Southern College, where the Marguerite Jones Harbert Building was named in her honor. She was also inducted into its Sports Hall of Fame in 2006. She also served on the Boards of Trustees of the Birmingham Museum of Art and Cancer Comprehensive. Additionally, she served on the Board of Regents of the Smithsonian Institution.
She was educated at Mountain Brook Elementary School and Phillips High School. She graduated from Birmingham–Southern College, where she served as President of the Kappa Delta sorority chapter.