Ever since Bishop Stillingfleet accused John Locke of having unwittingly paved the way for the alleged heresy promulgated in John Toland's Christianity Not Mysterious, the latter two thinkers and works have been consistently joined in histories of philosophy covering the rise of natural religion in England. While scholars have generally thought that Locke got the better of the good bishop in their subsequent written exchanges initiated by the charge, they appear merely to assume that Stillingfleet correctly read Toland and that Locke accepts that reading. Perhaps the most obvious piece of evidence favouring that stance is that while Locke clearly admits 'above reason' doctrines, Toland dismisses them: Christianity is not mysterious! Through patient exposition of relevant texts and letters, deconstruction of scholarly works, and careful reasoning, Measuring the Distance between Locke and Toland shows that Toland's deviations from Locke regarding reason and faith are far more minor than anyone has concluded. Stillingfleet was correct to connect them, but was incorrect in the way that he did it.

In John Locke's Theology: An Ecumenical, Irenic, and Controversial Project, Jonathan S. Marko offers the closest work available to a theological system derived from the writings of John Locke. Marko argues that Locke's intent for The Reasonableness of Christianity, his most noted theological work, was to describe and defend his version of the fundamental doctrines of Christianity and not his personal theological views. Locke, Marko says, intended the work to be an ecumenical and irenic project during a controversial time in philosophy and theology. Locke described what qualifies someone as a Christian in simple and irenic terms, and argued for the necessity of Scripture and the reasonableness of God's means of conveying his authoritative messages. The Reasonableness of Christianity could be construed as personal, but mainly in the sense that it puts the burden of understanding Scripture and arriving at theological convictions on the autonomous individual, rejecting the notion that one should base one's doctrinal opinions on so-called authorities. His work was inadvertently controversial partly because then, like today, readers typically failed to make a distinction between Locke's personal and programmatic positions. Marko also points to places in Locke's corpus where he avoids advocating for a particular sectarian position in his treatment of theological doctrines. What is more, it shows why attempting to categorize Locke—a philosopher, theologian, and political scientist all at once—according to traditional Christian paradigms is a dangerous misstep and a difficult scholarly feat.