The phrase "freedom of conscience" is, of course, not to be found in the United States Constitution: the First Amendment says only that "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof." However, it seems probable that one, then-contemporary Protestant conception of freedom of conscience was presupposed in these two clauses. Evidence for this conjecture can be found not only in the debate and proposals concerning the Bill of Rights of the United States Constitution but also in the frequently more expansive language of early state constitutions.
Michael J. White,
The First Amendment's Religion Clauses: "Freedom of Conscience" Versus Institutional Accommodation,
San Diego L. Rev.
Available at: https://digital.sandiego.edu/sdlr/vol47/iss4/11