Edmund S. Morgan, an award-winning historian who illuminated the intellectual world of the Puritans, explored the paradox of freedom and slavery in colonial Virginia and, in his 80s, wrote a best-selling biography of Benjamin Franklin, died on Monday in New Haven. He was 97.

His death was confirmed by his editor, Robert Weil.

Like his mentor and fellow atheist, the Harvard historian Perry Miller, Professor Morgan found his richest material in the religious thought of Puritan New England and endless fascination in the theological debates and spiritual struggles of men like John Winthrop, Roger Williams and Ezra Stiles.

“I think that any group of people who have a system of belief that covers practically everything, and who act upon it, are bound to be interesting to any scholar,” he said in a 1987 interview with The William and Mary Quarterly....