Austin's most gothic novel was Cipher: A Romance (1869) which was published at the height of her relationship with Louisa May Alcott. Not surprisingly, this was the time when Alcott was pseudononymously publishing gothic horror short stories in periodicals. Cipher features illegitimate children, long lost relatives, poison, gypsies and more. Interestingly, in the dedication of Cipher, through the metaphor of launching a little craft into the river at which boys may throw missiles, Austin subtly acknowledges the control of the literary and public world by men, and acknowledges her hesitation at intruding into this world, but positive decision to do so. The Shadow of Moloch Mountain (1870) continued the adventure, gothic mode. In a review of this book, Harper's New Monthly Magazine stated "We confess to have followed with some interest the adventures of Beatrice and Marston Brent, and that it is quite impossible for even an experienced novel-reader to guess from one chapter what the next will bring forth" (Harper's March 1871 622).

Austin then published a collection of fairy tales intended primarily for children, Moonfolk, A True Account of the Home of the Fairy Tales (1874). Austin specifically intended Dora Darling, its sequel Outpost, Fairy Dreams and Moonfolk to be for children.

After this, Austin's style changed dramatically. She turned to writing realistic novels of Boston, Beacon Hill, and her Pilgrim ancestors. She published Mrs Beauchamp Brown (1880) about Boston high society, and The Desmond Hundred (1882).

Nantucket Scraps Being the Experience of an Off-Islander, in Season and Out of Season, Among a Passing People(1883) was quite popular, and demonstrates the height of Austin's realistic perception of the world around her. Nantucket Scraps has been described as some of her best writing, where, losing her tendency towards sensationalism, she writes an informative and readable account of the day-to-day life of the 1880s inhabitants of Nantucket as well as relating local legends and history. One more novel, The Story of a Storm (1886) was written before Austin started her famous "Pilgrim Stories."

The "Pilgrim Stories" actualized into four published books and a fifth partially written. They were the result of Jane's love and admiration for the stories she had heard since childhood and which her father, her brother, and she in turn spent considerable time researching. Growing up in a family which constantly reminded Austin of her Pilgrim ancestry, she felt the Pilgrim stories were her own history, the legacies of her own beginnings, and they inspired her to a level of achievement not always seen in her other work. Jane recalls her excitement at the Plymouth Rock: "the first flush of delight and surprise at discovering the wealth of romance imbedded in the 'Forefather's Rock' which to many observers still appears a mass of granite, stern, cold and sad" (David Alden preface). Austin frequently spent summers in Plymouth, visiting family landmarks and gathering information for her books. As can be seen from her letters to her publishers of 1891 and 1892, she typically spent the months of August and September at Plymouth Rock House. Plymouth Rock House, a popular resort, was located on the corners of North Street and Water Street (Davis 15). Pamphlet-guides of Plymouth, such as Handbook of Old Burial Hill, Plymouth Massachusetts and Guide to Historic Plymouth advertised five of Jane Austin's books in the back under the "Pilgrim Literature" section (her books were five of fourteen books advertised). It is not uncommon in Austin's books to find a footnote describing the history of a name or a location she uses or a verifying fact such as the museum where the sword she describes in Standish of Standish is stored. Austin's family records provided information on famous Pilgrims such as Miles Standish and John Alden as well as on lesser known characters that other of her books are based on, such as Le Baron of The Nameless Nobleman (1881).

The first "Pilgrim" book was Standish of Standish, A Story of the Pilgrims (1889). This book enjoyed tremendous success, going through at least 28 imprints, and was even dramatized in 1919 by Annie Russell Marble in Boston and New York (The National Union Catalog).

The other books in the Pilgrim series included Betty Alden: The First-Born Daughter of the Pilgrims (1891), A Nameless Nobleman (1881) (previously published, but chronologically placed here in the stories), and Dr. Le Baron and His Daughters, A Story of the Old Colony (1890). The first edition of Betty Alden was sold before it was off the press (Boston Globe 7), and an edition came out as late as 1919 (The National Union Catalog). Austin did extensive research into the legend that Betty Alden was the first white woman born in New England before writing the story. The National Union Catalog lists a copy of A Nameless Nobleman as being the 40th edition, and being in print as late as 1909. The Catholic World berates Austin for her depiction of Catholicism in this book:

It is a pity that a writer with so much talent for constructing an interesting story as is the author of the above could not have kept clear of matters of which she - for the writer is evidently of the novel writing sex - is not well informed. The idea of introducing an unscrupulous priest, who uses all sorts of doubtful means to accomplish what to him may appear a legitimate end, was worn threadbare a century ago. (August 1881, p 719)

Mother! For love of thee it was begun; In thy most honored name to-day 'tis done. And though all earthly cares must cease In that fair land of everlasting peace, Love aye is one, and they who love are one; Time cannot end what God in Time begun; And thou wilt joy e'en in thine endless rest, To know thy child obeys thy last behest.

Jane Goodwin Austin's style in these books is a careful combination of extensively researched fact filled in with fanciful imagination; as she phrased it, readers "shall not be misled as to facts, though these be strung upon a slender thread of romance" (Standish of Standish, "A Prefatory Note"). She was in the habit of including opening sections of explanation of historical facts at the beginning of many of her books. In the preface to David Alden, Austin specifically explains "nothing has been set down as fact that has not been carefully determined to be such." In the same preface, Austin even clears up a "somewhat sturdy popular error" that Governor Carver had a daughter in the Pilgrim settlement, a mistake caused by a gravestone that seemed to indicate this, by examining the recently rediscovered journal of Carver. In "A Word of Explanation" at the beginning of Dr. Le Baron and his Daughters, Austin writes "The tragedy embodied in chapter xxiv is also matter of history, and its veracity must apologize for its horror."

While writing the Pilgrim books, Austin continued to write gothic romances. These included Dolores, A Novel (1890), Queen Tempest (1890), The Twelve Great Diamonds, A Novel (1892), It Never Did Run Smooth, A Novel (1892), and The Cedar Swamp Mystery (1901, posthumously). In addition to these full length novels, Austin also wrote numerous short stories which appeared in periodicals, such as "Women's Hair: As Glory and As Property" in January 1881 Frank Leslie's Popular Monthlem , The Atlantic, and Harper's New Monthly Magazine. She also wrote selections for specific compilations, such as for Famous Fiction by the World's Greatest Authors Famous Fiction Series (1894), and Twenty Complete Novelettes by Popular Authors (1894). Austin also published poetry, for example in The Poet's Year (1890) edited by Oscar Fay Adams.