In addition to novels, she wrote short stories, essays, and articles for magazines and newspapers on such issues as feminism, politics, and war.

William Sharp wrote in The Spectator praising her fiction and would later invite Atherton to stay with him and his wife, Elizabeth, in South Hampstead.

In an 1899 article for London's Bookman, Atherton wrote of Wilde's style and associated it with "the decadence, the loss of virility that must follow over-civilization."

In 1891, while writing a weekly column for The San Francisco Examiner, she met Ambrose Bierce, with whom she carried on a taunting, tumultuous friendship.

The story (set in the 1840s) focuses on Chonita Moncada y Iturbi and her love of Diego Estenega (modeled after Mariano Guadalupe Vallejo), as he dreams of modernizing California, retaining its Mexican character without sacrificing American economic vigor.

She also wrote letters to Bierce, confiding her loneliness, her dismay at the necessity to do freelance writing (in particular for the New York World), and her dislike of eastern literary circles.

Max Pemberton asked her to write a 10,000 word essay for a series he was editing for Cassells Pocket Library, which she wrote as A Whirl Asunder (1895).

In the May 15 issue of The New York Times, the reviewer said that Atherton had "incontestable" ability and a "very original talent" while noting that the book offered a series of "fleshy" episodes in Patience's life that may scare a sensitive reader.

Critics received this much more positively than Patience, and a review in The Spectator (October 1, 1898) said it "was by far more convincing and attractive in delineating California manners and morals....

The novel fairly establishes her claim to be considered as one of the most vivid and entertaining interpreters of the complex characters of emancipated American womanhood."

in the North American Review, Atherton critiqued William Dean Howells for the "littleism" or "thin" realism of his fiction.

Some say that 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.

However, its view of gender issues is nuanced: she mentioned "the happy fate of the American woman, who 'had things all her own way,' and to whom man was a slave."

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.

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".

Among her celebrity friends was travel writer Richard Halliburton, who shared her interest in artists' rights, and whose disappearance at sea she lamented.

[19] Though she could be offensively assertive with her acerbic wit, notes Gerry Max, she crusaded with dertermination 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.

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".

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.

[21] 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".

"[22] 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.

[26][28] 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'".

[30] Atherton's autobiography, Adventures of a Novelist (New York: Horace Liveright, 1932), is an account of her life and the people she knew, including Ambrose Bierce and James Phelan.

In 2009, The Library of America selected Atherton's story "The Striding Place" for inclusion in its two-century retrospective of American Fantastic Tales.