While working as Assistant Church Historian, he co-authored The Story of the Latter-day Saints with Glen Leonard.
Allen resigned as Assistant Church Historian in 1979, returning to work at Brigham Young University (BYU) full-time.
After his retirement in 1992, he was a senior research fellow at the Joseph Fielding Smith Institute for Latter-day Saint History.
Allen's paper from that seminar was published in Utah Historical Quarterly in 1955 and became the basis for his graduate studies.
In 1956, his thesis, The Development of County Government in the Territory of Utah, 1850-1896,[7] which drew from his earlier published article, was completed.
[3] His dissertation, The Company Town in the American West, was later published as a book by the University of Oklahoma Press.
From 1992 to 2005, he was a senior research fellow with BYU's Joseph Fielding Smith Institute for Latter-day Saint History and served on its executive committee for a time.
[15] Representing the MHA, Allen wrote and edited the "Historian's Corner," a semi-annual column in the quarterly BYU Studies from 1970 to 1982, when he was succeeded by Ronald W.
[5] Arrington had assembled a team of professional historians to engage in new academic research with use of the church archives.
[20] Ezra Taft Benson denounced the book as new history that was "underplaying revelation"[21] at a fireside and later, at an address for CES instructors.
[2] Allen served in the LDS Church throughout his life, including as a bishop of a student ward at BYU in the 1960s[10] and a stake high councilor.
[23] Orson Scott Card cites his admiration for Allen as having "the kind of skepticism [...] that is a servant to orthodox faith.