In addition to philosophy, Boyle devoted much time to theology, showing a very decided leaning to the practical side and an indifference to controversial polemics. At the Restoration of the king in 1660, he was favourably received at court and in 1665 would have received the provostship of Eton College had he agreed to take holy orders, but this he refused to do on the ground that his writings on religious subjects would have greater weight coming from a layman than a paid minister of the Church.
Moreover, Boyle incorporated his scientific interests into his theology, believing that natural philosophy could provide powerful evidence for the existence of God. In works such as Disquisition about the Final Causes of Natural Things (1688), for instance, he criticised contemporary philosophers – such as René Descartes – who denied that the study of nature could reveal much about God. Instead, Boyle argued that natural philosophers could use the design apparently on display in some parts of nature to demonstrate Gods involvement with the world. He also attempted to tackle complex theological questions using methods derived from his scientific practices. In Some Physico-Theological Considerations about the Possibility of the Resurrection' (1675), he used a chemical experiment known as the reduction to the pristine state as part of an attempt to demonstrate the physical possibility of the resurrection of the body. Throughout his career, Boyle tried to show that science could lend support to Christianity.
As a director of the East India Company he spent large sums in promoting the spread of Christianity in the East, contributing liberally to missionary societies and to the expenses of translating the Bible or portions of it into various languages. Boyle supported the policy that the Bible should be available in the vernacular language of the people. An Irish language version of the New Testament was published in 1602 but was rare in Boyles adult life. In 1680–85 Boyle personally financed the printing of the Bible, both Old and New Testaments, in Irish. In this respect, Boyles attitude to the Irish language differed from the Protestant Ascendancy class in Ireland at the time, which was generally hostile to the language and largely opposed the use of Irish (not only as a language of religious worship).
Boyle also had a monogenist perspective about race origin. He was a pioneer studying races, and he believed that all human beings, no matter how diverse their physical differences, came from the same source: Adam and Eve. He studied reported stories of parents giving birth to different coloured albinos, so he concluded that Adam and Eve were originally white and that Caucasians could give birth to different coloured races. Boyle also extended the theories of Robert Hooke and Isaac Newton about colour and light via optical projection (in physics) into discourses of polygenesis, speculating that maybe these differences were due to "seminal impressions". Taking this into account, it might be considered that he envisioned a good explanation for complexion at his time, due to the fact that now we know that skin colour is disposed by genes, which are actually contained in the semen. Boyles writings mention that at his time, for "European Eyes", beauty was not measured so much in colour of skin, but in "stature, comely symmetry of the parts of the body, and good features in the face". Various members of the scientific community rejected his views and described them as "disturbing" or "amusing".
In his will, Boyle provided money for a series of lectures to defend the Christian religion against those he considered "notorious infidels, namely atheists, deists, pagans, Jews and Muslims", with the provision that controversies between Christians were not to be mentioned (see Boyle Lectures).