She traveled to Rouen and wrote American Wives and English Husbands (1898), set in contemporary time. In this novel, she contrasts English and American men, American and English civilizations, and comments on the relationships between men and women. She also completed The Valiant Runaways (1898), an adventure novel for boys that dealt with the Spanish Mexican attempt to civilize California. In 1899, she returned to the United States.
Her novel Senator North (1900) was based on Maine's senator Eugene Hale.
In a May 1904 article, Why Is American Literature Bourgeois? in the North American Review, Atherton critiqued William Dean Howells for the "littleism" or "thin" realism of his fiction. Atherton's novel, Julia France and Her Times (1912), has a strong feminist subtext, with the titular heroine being a woman needing to earn a living wage.
She is best remembered for her California Series, several novels and short stories dealing with the social history of California. The series includes The Splendid, Idle Forties (1902); The Conqueror (1902), which is a fictionalized biography of Alexander Hamilton; and her sensational, semi-autobiographical novel Black Oxen (1923), about an aging woman who miraculously becomes young again after glandular therapy. The novel names the areas of a woman's power as youth and vitality, examines the social expectations surrounding them, then prompts women to avoid these conventions. The latter was adapted into the film Black Oxen in 1923. Atherton's earlier novel Mrs. Balfame (1916) was also adapted to film, as Mrs. Balfame in 1917. Atherton's The Immortal Marriage (1927) and The Jealous Gods (1928) are historical novels set in Ancient Greece.
Atherton wrote several stories of supernatural horror, including the ghost stories "Death and the Woman", and "Crowned with One Crest", as well as "The Foghorn", and the often anthologised "The Striding Place". "The Foghorn", written in 1933, is a psychological horror story that has been compared to "The Yellow Wallpaper". W. Somerset Maugham called it a powerful story in a 1943 publication of his, Great Modern Reading.
Atherton was an early feminist well acquainted with the plight of women. She knew "the pain of sexual repression, knew the cost of strength required to escape it (strength some women do not have to spend), knew its scars—the scars that made her wary of emotional commitment and relegated her, despite her splendid professional triumphs and her surpassing benefit to women, to largely an observer role in human relations. She knew the full cost of the destructive battle of the sexes, and urged that it end at last with true sexual equality." Her novels often feature strong heroines who pursue independent lives, undoubtedly a reaction to her stifling married life.
Atherton was often compared to contemporary authors such as Henry James and Edith Wharton. James assessed Atherton's work and claimed she had reduced the typical man/woman relationship to a personality clash.
Atherton presided in her last years over the San Francisco branch of PEN. As her biographer Emily Wortis Leider notes in California's Daughter, however, "under her domination it became little more than a social club that might have been called Friends of Atherton and (Senator) Phelan". A strong advocate of social reform, and the grande dame of California literature, she yet remained a strong force in the promotion of a California cultural identity. She was a personal friend of Senator James Duval Phelan and his nephew, the philanthropist Noel Sullivan, and often was a guest at Phelan's estate, Villa Montalvo. Among her celebrity friends was travel writer Richard Halliburton, who shared her interest in artists' rights, and whose disappearance at sea she lamented. Though she could be offensively assertive with her acerbic wit, notes Gerry Max, she truculently crusaded for many of the key intellectual freedom issues of her day, especially those involving women's rights, and remained, throughout a long creative life, a true friend to writers. In his autobiographical novel, Kenneth Rexroth speaks of her kindness to him and his wife when they arrived in San Francisco in the late 1920s.
Mariana Bertola, Carrie Jacobs-Bond, May Showler Groves, Minna McGauley, Maud Wilde, Jeanette Lawrence, Miriam Van Waters, Mrs. David Starr Jordan, Annie Florence Brown, Gertrude Atherton
Charlotte S. McClure in a Dictionary of Literary Biography essay said that Atherton "redefined women's potential and presented a psychological drama of a woman's quest for identity and for a life purpose and happiness within and beyond her procreative function". She also said that Patience Sparhawk was Atherton's "first significant novel".In an 1898 essay in Bookman, a critic stated:
"the amazing and memorable Patience Sparhawk may perhaps be referred to as the first foreshadowing of the good work that [Atherton] has done since. It seems to have been also generally conceded that no matter what the subject chanced to be . . . nothing from her pen would be commonplace or dull. that startling performance [in Patience Sparhawk] introduced her to a different audience, one much larger and more seriously interested than she had had before."
Carl van Vechten said of Atherton in a Nation article: "Usually (not always, to be sure), the work of Mrs. Wharton seems to me to be scrupulous, clever and uninspiring, while that of Mrs. Atherton is often careless, sprawling, but inspired. Mrs. Wharton, with some difficulty, it would appear, has learned to write; Mrs. Atherton was born with a facility for telling stories."
In an essay for Bookman, Frederic Taber Cooper stated that in Senator North, the character Harriet "is practically a white woman but for a scarcely perceptible blueness at the base of her fingernails, this character of Harriet is perhaps the best bit of feminine analysis that Mrs. Atherton ever did."
Atherton was a suffragist who did not believe in the use of militancy to further the cause. In 1917 she wrote a letter to the editor of the New York Times to express her support for suffrage while voicing her opposition to militancy.
Atherton also advocated white supremacy. Atherton's novel Senator North describes a marriage between a "passing" woman of mixed white and African-American ancestry and a white man, which ends in tragedy. Senator North was intended by Atherton as a warning against Interracial marriages. In a 1922 The Bookman article, "The Alpine School of Fiction", Atherton praised the book The Passing of the Great Race by Madison Grant, describing it as a "remarkable work, with its warning of tremendous import to civilization". Atherton claimed that American civilization had been created by the "Nordic" or "Anglo-Saxon" race, and that this was now threatened by an influx of "Alpine" and "Mediterranean" immigrants, who Atherton regarded as inferior to Nordics. Atherton argued that "The old Nordic-American stock is being rapidly bred out by the refuse of Europe." Atherton cited works such as Main Street by Sinclair Lewis and Three Soldiers by John Dos Passos as signs of a decline in American literature brought about by the rejection of "Nordic" themes. Atherton's views on race were praised by Thomas Dixon Jr., but strongly criticized by both H. L. Mencken and Horace Kallen.
Following the Russian Revolution, Atherton developed a hostility to Communism. In 1919, Atherton wrote an article for The New York Times, (entitled "Time as a cure for Bolshevism") which condemned both the Russian Soviet Federative Socialist Republic and the Americans who sympathized with it. When asked by the League of American Writers which side she supported in the Spanish Civil War, she stated that she supported the Spanish Nationalists-the only author of the 418 the League surveyed who did. In the League pamphlet Writers Take Sides (collecting the authors' responses), Atherton stated that although she disliked both fascism and communism, she considered communism the greater evil and added, "Although I have no love for Franco, I hope he will mop up the Communists, and send home, with tails between legs, all those gullible Americans who enlisted to save Spanish 'Democracy'". In a poll carried out by the Saturday Review of Literature asking writers which Presidential candidate they endorsed in the 1940 election, Atherton was among the writers who endorsed Wendell Willkie.
Atherton's autobiography, Adventures of a Novelist (New York: Horace Liveright, 1932), is an account of her life and the people, including Ambrose Bierce and James Phelan, who filled it. It also features historical reminiscences of San Francisco in the late 19th and early 20th centuries.
She is buried in Cypress Lawn cemetery in Colma, California. In 2009, The Library of America selected Atherton's story "The Striding Place" for inclusion in its