Allen was born on the Cubero Spanish-Mexican land grant in New Mexico to a Laguna-Sioux-Scottish mother and a Lebanese-American father. After attending several colleges in New Mexico and Colorado, she received a B.A. in English from the University of Oregon in 1966 and an M.F.A. in creative writing two years later. During this time, she married, became a mother, and divorced. She then went to the University of New Mexico in Albuquerque, and in 1975 completed a Ph.D. in American Studies with an emphasis in Native-American Studies.

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By the early 1980s, Allen had achieved significant recognition as a Native-American poet, literary scholar, and spokesperson. Her introduction to The Sacred Hoop: Recovering the Feminine in American Indian Traditions (1986) indicates an important shift in her career, for in it she comes out as a lesbian.

Allen has received a number of awards, including a National Endowment for the Arts Creative Writing Fellowship (1978), a post-doctoral fellowship at the University of California, Los Angeles (1980-1981), and a post-doctoral research grant from the Ford Foundation (1984-1985). She has taught English and Native-American Studies at the University of New Mexico, Stanford University, the University of California, Berkeley, and the University of California, Los Angeles.

Allen's culturally mixed heritage greatly influences her work as a poet, fiction writer, and literary scholar. In both her creative and critical writings, she reinterprets the historic and mythic beliefs of indigenous North American peoples from a twentieth-century lesbian-feminist perspective and develops a highly distinctive, woman-focused, non-heterosexist tradition. By incorporating Native-American accounts of a cosmic feminine power into her poetry, she connects the past with the present and creates a complex pattern of continuity, regeneration, and change that affirms her gynecentric spirit-based overview.

In "Some Like Indians Endure," for example, she associates lesbians with Native Americans in order to underscore the importance of maintaining a self-empowering visionary belief in the interconnectedness of all things. Relatedly, her novel, The Woman Who Owned the Shadows (1983), explores the cultural, sexual, and spiritual fragmentation experienced by those who have become disconnected from this overarching life force.

Allen has played a pivotal role in redefining scholarly views of traditional and contemporary Native-American sexualities. In "Hwame, Koshkalaka, and the Rest: Lesbians in American Indian Cultures" and several other essays collected in The Sacred Hoop, she argues that European colonizers and Western-trained ethnographers erased or otherwise distorted evidence of same-sex relationships in tribal cultures.

Her unique mythic system, described in The Sacred Hoop and Grandmothers of the Light (1991), represents an innovative departure from the heterosexual bias found in most mythologies. By incorporating aspects of Keres, Navajo, and other Native-American theologies into her revisionist myths, she distinguishes between (hetero)sexual biological reproduction and other forms of creativity.

Allen's work as an editor and literary scholar, along with her willingness to identify herself as lesbian in print, has enabled her to make important contributions to the careers of other lesbian and gay American-Indian writers.

Since Stonewall various political agendas have dominated American lesbian literature.

From the two-spirits of traditional culture to contemporary writers, Native North Americans have produced a considerable body of gay and lesbian literature.

Since the 1960s, the general trend in lesbian poetry has been collective and political rather than purely aesthetic.