Muller's research and writing has been largely focused on the reassessment of the development of Protestant thought after the Reformation, with emphasis on the nature and character of Protestant orthodoxy and Reformed scholasticism in the seventeenth century. Muller is one of the historians credited with setting aside the "Calvin against the Calvinists" theory of developing Reformed thought. His argument is that the attempt to define the entire Reformed tradition in terms of the thought of Calvin is a historical error, inasmuch as Calvin was one of several second generation codifiers of the tradition and inasmuch as the tradition itself was, early on, rather diverse and variegated. The "Calvin against the Calvinists" thesis tended to claim in a rather reductionistic way that Calvin was a "christocentric" theologian in contrast to later Reformed thinkers who had developed a radical predestinarian or deterministic metaphysics. By contrast Muller has argued that the later Reformed thinkers did not develop a predestinarian system but instead understood theology in terms of a series of biblically and traditionally based loci or topics. Their thought does differ in places from Calvin's, but the differences are to be explained on the basis of other sources of the Reformed tradition, such as the thought of Martin Bucer, Heinrich Bullinger, Peter Martyr Vermigli, and others, on the basis of alterations in debate and historical context.
^See Martin I. Klauber, "Continuity and Discontinuity in Post-Reformation Reformed Theology: an evaluation of the Muller Thesis," in Journal of the Evangelical Theological Society, 33 (1990): 467-475; and W. J. van Asselt, et al., Inleiding in de Gereformeerde Scholastiek, (Zoetermeer: Boekencentrum, 1998): 28, 73-74, 91-92.
^Richard A. Muller, "John Calvin and later Calvinism: the identity of the Reformed Tradition," in The Cambridge Companion to Reformation Theology, edited by David Bagchi and David C. Steinmetz (Cambridge: Cambridge University Press, 2004): 130-149.
van Asselt, Willem J. (2010). Introduction to Reformed Scholasticism. With contributions by T. Theo J. Pleizier, Pieter L. Rouwendal, and Maarten Wisse; Translated by Albert Gootjes. Grand Rapids, Michigan: Reformation Heritage Books. ISBN978-1-60178-121-5.
Bagchi, David and David C. Steinmetz, eds., The Cambridge Companion to Reformation Theology. Cambridge: Cambridge University Press, 2004.
Klauber, Martin I. "Continuity and Discontinuity in Post-Reformation Reformed Theology: an evaluation of the Muller Thesis," in Journal of the Evangelical Theological Society, 33 (1990): 467-475.