In 1565 hundreds of French Protestants were systematically wiped out by Spanish conquistador Menéndez--specifically for refusing to re-convert to Rome--at what is now Fort Matanzas. Menéndez then established St. Augustine.
A National Monument to that event exists there today--you can read about it here.
That Spanish killed French in the New World is not in dispute, but the reasons were commercial and territorial, not theological. In the context of religious, territorial and trade wars raging across Europe those Protestants had invaded Spanish territory and had established an armed fort and were protecting it with a fleet of 11 ships. The presence of a foreign fort and fleet were a direct threat to the Spanish treasure fleets sailing to and from Spain. Name one 16th sovereign of any religion that would not have responded similarly with force.