Locke was a mortalist, as he argued that the soul dies with the body. He thought that the resurrection of the dead will take place by divine miracle on Judgment Day, when the saved will be admitted to eternal beatitude while the wicked will experience a second, final death. He was also agnostic about the ontological constitution of thinking substances or souls. Moreover, he questioned the resurrection of the body, since he argued that our corruptible, mortal bodies will be changed into incorruptible, spiritual bodies at resurrection. Locke’s position on the soul and the resurrection of the dead implies that personal identity is neither in the soul, nor in the body, nor in a union of soul and body. In "Essay" II.xxvii (1694, 2nd ed.), he argued that consciousness alone makes personal identity. To Locke, the same self exists diachronically, in this life and beyond it, “by the same consciousness.” However, Locke’s “annexing” of punishment to personality, and of personality to consciousness, does not contradict his notion of repentance, for he saw repentance as necessary but not sufficient to salvation and, emphasizing faith, he believed in God’s forgiveness of the repentant faithful.

Locke’s doctrine of the fundamentals has important irenic implications. His omission of disputed doctrines from his account of Christianity implies toleration of all those accepting the Law of Faith. Moreover, his theological writings do not describe affiliation to a church as essential to salvation. This position implicitly makes denominationally uncommitted Christians tolerable. This is a step beyond the mere separation between the state and religious societies, which Locke affirmed in his “letters” on toleration. However, Locke argued that acceptance of the Law of Faith could lead not only to salvation, but also to properly comprehend and observe the divine law. This position is problematic, since Locke avoided extending toleration from competing conceptions of salvation to competing conceptions of the good. But, to Locke, those who believe in God, although rejecting the Law of Faith, are tolerable, because they acknowledge the divinely given Law of Nature and, thus, can meet at least minimally decent moral standards. This is why he did not exclude non-Christian believers from toleration, while he was intolerant of atheists and censured the immoral ideas held by Roman Catholics.

Whereas John Locke (1632–1704) is best known for his "way of ideas" and political theory, he was also a skilled theologian. His theological concerns, interests, and ideas permeate his philosophical, political, and moral thought. Locke’s oeuvre in its different areas is indeed the production of a Christian philosopher. But Locke’s religious views are significant for yet another reason, in that his theological reflections resulted in a unique version of Christianity. Although Locke expounded his religious views in an unsystematic manner, given also his dislike of systems of doctrine and his hostility to claims of religious orthodoxy, an original and internally coherent form of Protestant Christianity emerges from his public as well as private writings. Locke's version of Christianity denotes various similarities with heterodox theological currents such as Socinianism and Arminianism, which Locke knew well. Nonetheless, Locke adhered to the Protestant doctrine of "sola Scriptura," according to which the Scriptures contain all that is needed for salvation. Thus, he always made sure that his conclusions were consistent with, and indeed grounded in, Scripture.

In "The Reasonableness of Christianity," Locke aimed to promote the practice of morality and the development of moral character through a Scripture-based theological ethics. He claimed that his account of Christianity was based on Scripture alone, which he regarded as an authoritative source of historical and eschatological truth entailing moral principles. However, his writings on religion denote many similarities with Socinianism and Arminianism. He adopted Socinus’s proof of scriptural authority, highlighting the excellence of Christ’s moral precepts, insisting on the fulfillment of Old Testament Messianic prophecies in the New Testament, and describing Christ’s miracles as confirming his Messianic mission. This proof enabled Locke to develop a historical method of biblical interpretation, which, stressing the internal consistency of the Bible, considered the biblical texts in relation to both their respective historical contexts and the biblical discourse as a whole. In reading Scripture, he followed the Protestant tradition of the way of fundamentals, but he formulated an original doctrine of the fundamentals of Christianity – that is, repentance, obedience, and faith.

Locke regarded the Law of Nature as divinely given and, hence, inherently rational, universally binding, and eternally valid. This view of the Law of Nature informs his natural law theory, which presents both biblical and natural theological arguments. Yet, he believed in the superiority of the Law of Faith, delivered by Christ, over both the Law of Nature and the Law of Moses. To Locke, Christ not only affirmed the Law of Nature completely and unambiguously, but also assured humanity of otherworldly rewards and sanctions and of God’s forgiveness of the repentant faithful. Thus, the Law of Faith effectively promotes the practice of morality and the development of moral character and enables human beings to pursue salvation. Maintaining the necessity both of good works and of acceptance of God’s assisting grace for salvation, Locke rejected predestination, denied original sin, and excluded the satisfaction theory of atonement, which he described as a disputed doctrine, from his account of Christianity in his public writings. However, some of his manuscripts demonstrate his dislike for the satisfaction theory, to which he preferred the Arminians’ governmental theory of atonement.

Locke’s religion, although expounded unsystematically in his public as well as private writings, is an original and internally coherent version of Protestant Christianity, grounded in his painstaking analysis of Scripture. Locke’s endeavor as a theologian was typical of a biblical theologian who paid particular attention to the moral, soteriological, and eschatological meaning of Scripture, which he considered infallible. Moreover, virtually all areas of Locke's thought are pervaded by a religious dimension, and his reflections on several epistemological, moral, and political issues denote a markedly religious character. His religious views also influenced the development of various Protestant currents, such as Unitarianism, Baptism, and Methodism, despite the mixed reception that his thought met with among English divines in the late seventeenth and eighteenth century. Briefly, an accurate examination of Locke’s writings on religion, as well as his philosophical, moral, and political works, belies depicting him as a "secular" philosopher. Locke was the archetype of a "religious Enlightener" endorsing reasonable belief as the coordination of natural reason and divine revelation.

Locke omitted the Trinitarian dogma from his elucidation of the Christian religion in "The Reasonableness of Christianity." This omission implicitly made belief in the Trinity unnecessary to salvation and attracted much criticism, leading John Edwards and others to accuse Locke of Socinianism. Locke refused to clarify his position on the Trinity even when Edwards and Stillingfleet pressured him to do so. His public silence on the Trinity was surprising to many, because the "Reasonableness" appeared in the middle of the heated Trinitarian controversy of the late seventeenth century. Locke actually expressed, unsystematically and at times ambiguously, his views on Christ’s nature and mission in his public writings on religion and in various manuscript notes, and he focused on Trinitarian issues in "Adversaria Theologica" and other manuscripts. His Christological reflections and his consideration of Trinitarian issues denote a heterodox, non-Trinitarian conception of the Godhead, which presents both Socinian and Arian elements, although he never expressly denied the Trinity. Irenic and prudential reasons contributed to his choice to avoid public discussion of the Trinitarian dogma.

The "Reasonableness of Christianity" is Locke’s major book of theology. Before publishing this book in 1695, Locke always preferred to keep his religious ideas for himself. It was both his interest in some of the theological controversies of the day – particularly in the antinomian and deist controversies – and his effort to establish morality on convincing grounds that led him to turn to biblical theology. A markedly religious conception of life, however, conditioned his moral inquiry since the composition of the manuscript "Essays on the Law of Nature" (1664) and informed his reflections on morality in the "Second Treatise of Civil Government" and "An Essay concerning Human Understanding" (1690). In these works, Locke emphasized the necessity to believe in, and obey, a divine creator and legislator, and he described the moral law as God-given and, consequently, discoverable by natural reason (at least in principle) or through divine revelation. Nevertheless, Locke’s struggle to ground morality in theoretical foundations proved fruitless and eventually led him to turn, in the "Reasonableness," to a Scripture-based theological ethics in order to promote moral practice.