Isaac Allerton may have come from the vicinity of Ipswich, co. Suffolk, England. He first appears in Leiden, Holland records on 4 November 1611, when he married Mary Norris. Isaac had a sister named Sarah who also resided in Leiden, and who married future Mayflower passenger Degory Priest. He was probably also related, perhaps a brother, to Mayflower passenger John Allerton.
Isaac Allerton is one of the most complex figures in early Plymouth Colony. He was elected assistant to Governor Bradford in 1621, and continued in that capacity well into the 1630s. He was the individual sent to handle most of the buyout negotiations with the London investors that ccommenced in 1627, and continued through the early 1630s. Allerton soon began to take advantage of his position by engaging in some personal trading deals, and engaging the Pilgrims' joint-stock company in business ventures they had not authorized. After driving the colony deeper into debt with ill-advised business opportunities, he was eventually removed and replaced by Edward Winslow. After the death of his wife Fear in 1634, he retreated to the New Haven Colony and married there to Joanna Swinnerton.
Allerton became an active merchant trader, engaging in transactions and trade with many neighboring colonies including the Dutch at New Netherlands; New Sweden; Virginia; Massachusetts Bay; and Barbados.