There were two prevailing sentiments in Europe after the Reformation: One opposing papal authority and one advocating individual freedom. This paper analyzes these two sentiments and finds that the concept of conscience is crucial in understanding them. The issue of conscience is about judging truth and good, and in initiating the Reformation, Martin Luther heavily appealed to his conscience while countering Catholic attacks. With the wide dispersal of the Reformation, Luther’s notion of conscience was well received among his supporters throughout Europe. Descartes later transformed Luther’s conscience into an epistemological being (the cogito), and argued that its existence was the only valid thing that survived his thorough skepticism — and as such is the foundation of human knowledge. Rousseau continued this line of thinking, which we call subjectivism, and re-employed the term conscience as a replacement for cogito, holding that conscience is the final authority in judging good and bad; that, as the starting point of human existence, it cannot be withheld from any human being; and that it therefore constitutes an inalienable human right. This paper argues that the Enlightenment was a subjectivist movement propelled by this conscience-cogito-conscience conceptualization, and that it sought to enlighten this inalienable conscience.