After his retirement from the war, Berrien engaged in privateering expeditions. This profession introduced him to Captain John Macpherson (1725-1792), a Scottish born privateer who amassed a fortune in the French and Indian Wars. Macpherson lavished his fortune on his home in Philadelphia, Mount Pleasant, considered one of the finest Georgian houses in the colonies.
Berrien fell in love with the captain's daughter Margaret Macpherson (1763-1785) and married her in 1780 in Philadelphia. After their marriage, Berrien and his new wife moved to Rockingham, where their son John Macpherson Berrien was born in 1781. In 1783, Berrien returned to Georgia with his wife and his infant son. Margaret died in McIntosh County, Georgia in 1785.
After returning to Georgia in 1783, Berrien served as justice of the peace and captain of the militia in Liberty County. He also acquired plantations through land lotteries from former Tory owners in Liberty and Franklin Counties. In 1786, the Georgia legislature appointed him Collector of Customs of the Port of Savannah; however, he lost re-election to this post in 1788.
After the death of his first wife in 1785, Berrien remarried. His second wife, Williamina Moore (1771-1838), came from an old Philadelphia family. In 1791, Berrien constructed his house on Broughton Street. While in Savannah, he served once again as Collector of Customs for the Port of Savannah, as well as alderman from 1791 to 1795.
Berrien was a member of Christ Church in Savannah and an original member of the Society of the Cincinnati, serving as a president of the Georgia Society. He was also a member of Solomon's Lodge, the masonic lodge founded in 1733 by James Oglethorpe. It is likely that the ballroom of the Berrien House hosted both groups.
In 1797, Berrien sold the Savannah house and became State Treasurer in the new state capital at Louisville. John Berrien died on November 6, 1815 in Savannah and now lies in Savannah's Colonial Cemetery, just a few short blocks from the Berrien House.