In September 1993, according to his biographer Lavina Fielding Anderson, his insubordination directed toward church authorities and his publication of his on-going work resulted in his excommunication from The Church of Jesus Christ of Latter-day Saints as one of the September Six. Despite his excommunication , Quinn believes in the Latter Day Saint movement, although he is in disagreement with certain policies and doctrines. He continues to be a widely-cited Mormon historian by researchers and students of Mormonism.

Quinn's research topics, both before and after his excommunication, were in-depth revisions of traditional accounts of Mormon history grounded in primary source material. Three of his most influential books, each of which is the focal point of intense controversy, are Early Mormonism and the Magic World View, The Mormon Hierarchy: Origins of Power, and The Mormon Hierarchy: Extensions of Power.

In an April 2006 article, Wall Street Journal reporter Daniel Golden wrote that Quinn has become unhireable because almost all the funding for professorships in Mormon studies comes from Mormon donors. In 2003, Brigham Young University threatened to withdraw funding for a conference it was co-sponsoring at Yale if Quinn were allowed to speak. More recently Arizona State University administrators vetoed the department of religious studies in its recommendation to hire Quinn. ASU faculty believe officials fear alienating ASU’s 3,700 LDS students and offending Ira Fulton, a powerful Mormon donor who, according to Golden, has called Quinn a “nothing person.”

In 2007, Quinn was interviewed in the PBS documentary The Mormons.

Early Mormonism and the Magic World View

Early Mormonism and the Magic World View is an exhaustive recounting of the role of 19th-century New England folk magic lore in Joseph Smith's early visions and in the development of the Book of Mormon. The book argues that Smith's early religious experiences were inextricably intermingled with ritual, supernaturalism, and white magic. Evidence is drawn from friendly firsthand sources, unfriendly firsthand sources, material artifacts, and parallels in ideas. All four sources agree that Joseph Smith used a collection of different seer stones in searching for buried treasure supposedly left by pirates, Spaniards, and Native Americans. The evidence suggests that these same seer stones were one of the primary tools used by Smith in translating the Book of Mormon. Likewise, evidence from all four categories of sources supports the idea that Smith approved of the use of rods for dowsing activities. Indeed, the first published version of an early revelation told Oliver Cowdery that a dowsing rod (referred to as a "rod of nature") would serve as a means of receiving divine revelation. Other claims, including Smith's purported involvement in astrology and the idea that the Book of Mormon guardian Moroni transformed from the form of a salamander, are less supported by evidence.

Some historians, both within and without the Mormon faith, consider this book an important contribution in understanding early Mormon history, and Quinn's supporters feel his work is groundbreaking. In a 1990 book review in Church History, Klaus J. Hansen calls the book a "magisterial study" and a "tour de force," and describes it as providing a "truly stunning mass of evidence" in favor of its position. John L. Brooke made Quinn's argument the starting point of his study, The Refiner's Fire : The Making of Mormon Cosmology, 1644-1844.

However, Mormon and non-Mormon scholars have also criticized the book as relying too heavily on environmental parallels without a proven connection to Smith's ideas and behavior, that it accepts at face value the disputed Howe-Hurlbut affidavits about Smith's New York reputation and behavior and a late 19th century newspaper account of a money-digging agreement involving Smith and his father, and that its central thesis is implausible without Mark Hofmann's "Salamander Letter"--which turned out to be a forgery. William J. Hamblin states in his review of the book that "the fact that Quinn could not discover a single primary source written by Latter-day Saints that makes any positive statement about magic is hardly dissuasive to a historian of Quinn's inventive capacity." An additional criticism suggests that the concept of magic is flawed and inherently subjective; it implies that Smith's use of seer stones and dowsing rods was superstitious or fraudulent rather than divine. However, some of Quinn's critics acknowledge that the book is "richly documented" (William A. Wilson in a 1989 book review in The Western Historical Quarterly) and an obligatory starting point for any discussion of Smith's involvement in 19th-century folkloric practices.

The Mormon Hierarchy

The two volumes of The Mormon Hierarchy provide a comprehensive secular organizational history of the church from its founding to modern times, and its influence on current LDS culture and doctrine. The work emphasizes conflict, coercion, and violence, especially during the 19th century (see Danites, Mountain Meadows massacre, Blood Atonement and Mormon War). During the 20th century, Quinn asserts his view that the church was increasing bureaucratization of the church, its role in right-wing anti-Communism during the 1960s, efforts against the Equal Rights Amendment, political work against same-sex marriage and some forms of anti-discrimination legislation, the church's mid-century financial crisis, conflicts over policies such as the so-called "baseball baptisms" of youth who knew little about the church, presumed disagreements among church Apostles that (Hugh B. Brown was open to rescinding the Negro doctrine in 1963, and attempted to rescind it in 1969, but was blocked from doing so by Harold B. Lee), and extensive business and family interrelationships among leaders.

In a review of The Mormon Hierarchy: Extensions of Power for the Foundation for Ancient Research and Mormon Studies, Duane Boyce asserts that there are scholarly deficiencies in the work and refers to it as a "betrayal of trust."

Same-Sex Dynamics among 19th-Century Mormons

Quinn has publicly argued that homosexual relationships, between both men and women, were quietly accepted by the Church of Jesus Christ of Latter-day Saints and its leadership up until the 1940s. This theme has arisen in Quinn's The Mormon Hierarchy: Extensions of Power and is the central topic of Same-Sex Dynamics Among Nineteenth-Century Americans: A Mormon Example. Several LDS scholars have disputed Quinn's work, calling it a distortion of LDS history and saying he completely misrepresented the facts. They deny any acceptance from previous leaders of homosexuality, suggesting that Quinn conflated an absence of early Church proscriptions of homosexuality with tacit acceptance of same, and state the current leadership of the church “is entirely consistent with the teachings of past leaders and with the scriptures.”

Quinn has edited a prominent collection of major publications in Mormon history over the last 40 years, The New Mormon History: Revisionist Essays on the Past. He has written and spoken about the parallels between 19th-century American attacks on Mormon polygamy and 20th- and 21st-century Mormon attacks on same-sex marriage. He has also presented an overview of recent biographies of Joseph Smith, suggesting that these biographies maintain an artificial division between Joseph Smith the treasure seeker and Joseph Smith the prophet.

Quinn is also a noteworthy biographer of the mid-20th-century Latter-day Saint leader J. Reuben Clark, Jr.. In two biographical volumes on the Mormon Apostle, Quinn has emphasized Clark's professional preeminence, his committed and sometimes inflexible leadership, his persistent pacifism and personal struggles.