To figure out whether the main empirical question “Is our brain hardwired to believe in and produce God, or is our brain hardwired to perceive and experience God?” is answered, this paper presents systematic critical review of the positions, arguments and controversies of each side of the neuroscientific–theological debate and puts forward an integral view where the human is seen as a psycho-somatic entity consisting of the multiple levels and dimensions of human existence (physical, biological, psychological, and spiritual reality), allowing consciousness/mind/spirit and brain/body/matter to be seen as different sides of the same phenomenon, neither reducible to each other. The emergence of a form of causation distinctive from physics where mental/conscious agency (a) is neither identical with nor reducible to brain processes and (b) does exert “downward” causal influence on brain plasticity and the various levels of brain functioning is discussed. This manuscript also discusses the role of cognitive processes in religious experience and outlines what can neuroscience offer for study of religious experience and what is the significance of this study for neuroscience, clinicians, theology and philosophy. A methodological shift from “explanation” to “description” of religious experience is suggested. This paper contributes to the ongoing discussion between theologians, cognitive psychologists and neuroscientists.