Allen's studies would eventually result in Recovering the Feminine in American Indian Traditions, a controversial text which argues that the accounts of Native beliefs and traditions were subverted by phallogocentric European explorers and colonizers, who downplayed or erased the central role that woman played in most Native societies. Allen argued that many Native tribes were "gynocratic", with women making the principal decisions, while others believed in absolute balance between male and female, with neither side gaining dominance.

Allen's arguments and research were much criticized in the years following publication of The Sacred Hoop. Gerald Vizenor and others have accused her of a simple reversal of essentialism, while historians and anthropologists have disproved or questioned some of her scholarship. However, her book and subsequent work also proved hugely influential, provoking an outpouring of feminist studies of Native cultures and literature. It remains a set text within many Native American Studies and Women's Studies programs.

Allen also wrote many essays of literary criticism. These often stress the sacredness of Native religions, attempting to ensure that these are treated as religions rather than being patronized as "folklore" or "myths".

Allen was well-known as a novelist, poet and short story writer. Her work, like that of fellow Laguna writer Leslie Marmon Silko, drew heavily on the Pueblo tales of Grandmother Spider and the Corn Maiden, and is noted for a strongly political streak.

Her novel, The Woman Who Owned The Shadows, was published in 1983. The story revolves around Ephanie, a mixed-blood like Allen herself, and her struggle to express herself creatively. As a poet, Allen's most successful collection so far is probably Life Is a Fatal Disease : Collected Poems 1962-1995. Allen has also been responsible for a number of collections of Native American writings, including Spider Womans Granddaughters: Traditional Tales and Contemporary Writing by Native American Women.

Allen's work has been categorized as belonging to the Native American Renaissance, though she herself rejected the label.

Allen was awarded an American Book Award by the Before Columbus Foundation, the Native American Prize for Literature, the Susan Koppelman Award, and in 2001 she was awarded a Lifetime Achievement Award by the Native Writers' Circle of the Americas.

Novels

• The Woman Who Owned The Shadows (1983)
• The Sacred Hoop: Recovering the Feminine in American Indian Traditions (1986)
• "Skin and Bones" is a book of poetry published years latter
• "Grandmothers of the light: A mesicine woman's sourcebook (1991)

Poetry

• Life is a Fatal Disease : Collected Poems 1962-1995 (1997)
• Skins and Bones : Poems 1979-1987 (1988)
• Shadow Country (1982)
• A Cannon Between My Knees (1981)
• Blind Lion Poems (or, The Blind Lion) (1974)

Academic

• Off the Reservation: Reflections on Boundary-Busting Border-Crossing Loose Canons (1998)
• Grandmothers of the Light: A Medicine Women's Sourcebook (1991)
• The Sacred Hoop: Recovering the Feminine in American Indian Traditions (1986)
• Studies in American Indian Literature: Critical Essays and Course Designs (1983)

Biography

• As Long As the Rivers Flow: The Stories of Nine Native Americans (1996)
• Pocahontas: Medicine Woman, Spy, Entrepreneur, Diplomat (2004)

Edited Collections and Anthologies

• Hozho: Walking in Beauty: Short Stories by American Indian Writers (2001)
• Song of the Turtle: American Indian Literature, 1974-1994 (1996)
• Voice of the Turtle: American Indian Literature 1900-1970 (1994)
• Spider Woman's Granddaughters: Traditional Tales and Contemporary Writing by Native American Women (1989)

Anthology Contributions

• Living the Spirit: A Gay American Indian Anthology, ed. Will Roscoe. (1988)

• The Serpent's Tongue: Prose, Poetry, and Art of the New Mexican Pueblos, ed. Nancy Wood. (1997)