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.
Early in the 1660s Berry’s family and friends arranged for him to be appointed boatswain of the naval vessel Swallow, which in 1663 sailed to Jamaica. Berry won rapid promotions in the Caribbean during the Second Anglo-Dutch War. As commanding officer of the Mary in 1665 he captured thirty-two prizes in four months, and in 1667 he commanded a fleet of ten ships that defeated thirty French and Dutch vessels at Nevis. Berry later commanded English warships in action against the Algerine pirates in the Mediterranean. During the Third Anglo-Dutch War he commanded the Resolution at the Battle of Sole Bay and rescued James Stuart, the duke of York, for which Charles II knighted him immediately after the battle and made him governor of Deal Castle. Berry also distinguished himself at the Battle of Dogger Bank in May 1673 and later served again in the Mediterranean. He also investigated conditions in the Newfoundland fisheries in 1675 and submitted to the Admiralty a plan for governing the island.
In October 1676 the king named Berry to a commission that led an armed force of ten naval vessels and more than 1,000 soldiers to put down Bacon’s Rebellion in Virginia and to investigate its causes. The commissioners were Berry, who commanded the fleet, Colonel Herbert Jeffreys, in charge of the soldiers, and Virginian Francis Moryson. Berry and Jeffreys preceded the main body of the force to Virginia, but by the time Berry’s flagship, the Bristol, dropped anchor in the James River on January 29, 1677, the rebellion was already over. The commissioners informed Governor Sir William Berkeley that the other ships and the remainder of the armed force were en route to the colony, that he should issue a royal pardon to the participants in the rebellion, and that he should step down as governor. Relations between the governor and the commissioners were marked by hostility, suspicion, and cross purposes as the latter attempted to follow their instructions to impose order on the colony that Berkeley insisted was already pacified. Moryson took office as lieutenant governor when Berkeley left Virginia for England in the spring, and by June 1677 Berry’s crew was so ill that he decided to disregard his additional instructions to go to New England and assist royal officials there in the aftermath of what was called King Philip’s War. Instead, Berry sailed for London.
Berry was an able and brave naval officer. He saved the life of the duke of York a second time in 1682, and in 1684 he was named one of the commissioners who discharged the duties of the lord high admiral of England after the duke of York was obliged to surrender the office because of his Catholicism. After the duke succeeded to the throne asin 1685, Berry was a royal favorite and was promoted to rear admiral in September 1688 and to vice admiral in December of that year. He nevertheless led the Protestant naval officers during the revolution that replaced James II with William and Mary. Berry remained one of the commissioners of the navy and became close to the new king, who appointed him comptroller of the victualling accounts.
Berry and his wife, Lady Rebecca Berry, had one daughter who was born in 1667 but died young. Sir John Berry died at Portsmouth, England, on February 14, 1690. Physicians who examined his body declared that he had been poisoned, but no one was prosecuted for murder, and he may actually have died of a fever. He was buried on February 21, 1690, in Stepney Church near London.