Berry was born near South Molton in Devonshire, England, the second of seven sons and one of nine children of Elizabeth Moore Berry and Daniel Berry, the vicar of Molland and Knowstone. He was christened on January 7, 1636, in his father’s Knowstone Parish. In 1652, because of Daniel Berry’s loyalty to the Crown and devotion to the Church of England, local supporters of the Commonwealth drove him from his church and vicarage. John Berry went to sea on a merchant ship out of Plymouth, but a Spanish vessel captured him, and he did not return to England for several years.