Allen, James B.. "The Story of The Truth, The Way, The Life." In The Truth, The Way, the Life: An Elementary Treatise on Theology, edited by John W. Welch, 680-720. 2nd ed. Provo, UT: BYU Studies, 1996.

Allen, James B.. Mormon Scholars Testify: James B. Allen - "Some Things I Believe, and Why". Mormon Scholars Testify, 2010.

Allen, James B.. "Asked and Answered: A Response to Grant H. Palmer." The FARMS Review 16, no. 1 (2004): 235-285.

Allen, James B.. "Davis Bitton: His Scholarship and Faith." The FARMS Review 19, no. 1 (2007): 1-8.

Allen, James B.. "The Rise and Decline of the LDS Indian Student Placement Program, 1947-1996." In Mormons, Scripture, and the Ancient World: Studies in Honor of John L. Sorenson, edited by Davis Bitton, 85-119. Provo, UT: Foundation for Ancient Research and Mormon Studies, 1998.

Allen, James B.. "Eight Contemporary Accounts of Joseph Smith's First Vision - What Do We Learn from Them? ." Improvement Era 73, no. 4 (1970): 4-13.

Allen, James B., and John W. Welch. "Analysis of Joseph Smith's Accounts of His First Vision." In Opening the Heavens: Accounts of Divine Manifestation, 1820-1844, edited by John W. Welch, 36-77. 2nd ed. Provo, UT/Salt Lake City: BYU Press/Deseret Book, 2017.

Allen, James B., and John W. Welch. "Analysis of Joseph Smith’s Accounts of His First Vision." In Opening the Heavens: Accounts of Divine Manifestation, 1820-1844, edited by John W. Welch, 36-77. 2nd ed. Provo, UT/Salt Lake City: Brigham Young University Press/Deseret Book, 2017.

Allen, James B.. "Second Only to Christ: Joseph Smith in Modern Mormon Piety." In The Disciple as Witness Essays on Latter-day Saint History and Doctrine in Honor of Richard Lloyd Anderson, edited by Stephen D. Ricks, Donald W. Parry and Andrew H. Hedges, 1-35. Provo, UT: Foundation for Ancient Research and Mormon Studies, 2000.

Allen, James B.. "Joseph Smith Papers, Revelations and Translations, Volume 3: Printer’s Manuscript of the Book of Mormon Edited by Royal Skousen and Robin Scott Jensen." BYU Studies Quarterly 59, no. 2 (2020): 311-317.

Allen, James B., and Malcolm R. Thorp. "The Mission of the Twelve to England, 1840–41: Mormon Apostles and the Working Classes." BYU Studies Quarterly 15, no. 4 (1975): 499-526.

Allen, James B.. "To the Saints in England: Impressions of a Mormon Immigrant." BYU Studies Quarterly 18, no. 3 (1978): 475-480.