Even before the English colonists reached Virginia in 1607, they had created their first prisoner. John Smith was so outspoken during the journey from London to Virginia that after the three-vessel expedition resupplied at the Canary Islands, the other leaders of the expedition accused Smith of mutiny and decided to hang him. Smith wrote later1 that he was "restrained" for the rest of the trip, so it is possible that the first prison in Virginia was his cabin on the Susan Constant as it sailed into the Chesaeake Bay.
In the close quarters of the ships during an ocean journey, it is more likely that restraint consisted of a loss of status and shunning by the leaders who had tired of hearing his advice, rather than physical imprisonment in chains or in any form of shipboard jail. Room on those ships was very scarce - giving Smith a private cabin as a cell would not have been a punishment...
Upon arrival in the New World, the unhappy leaders lost their nerve - or were restrained by Captain Christopher Newport, who had been given command during the trip across the Atlantic Ocean. Instead of being hung, Smith led explorations into unknown territory soon after the colonists determined to settle at Jamestown. However, it took Smith two months before he was seated on the council that the London Company had designated to govern the colony.
By September 1607, just five months after the English started unpacking from the three ships and building James Fort, the colony needed a prison.
The first two English prisoners in Virginia were political leaders - Edward Maria Wingfield, the President of the Council, and George Kendall, a member of the council. The council rebelled against Wingfield in September 1607. The councillors removed him from the presidency and placed him under arrest - but that required the colony to have a secure facility.
Wingfield was taken away from from the fort at Jamestown and incarcerated on the Discovery. That ship had carried 21 passengers across the Atlantic Ocean for over three months, and it was about the size of a modern singlewide house trailer. (The larger Godspeed and Susan Constant had already returned to England with Captain Newport in July.)
Placing a prisoner on Discovery limited Wingfield's mobility and blocked him from communicating with most other colonists. He remained imprisoned there for about as long as the original trip from England to Virginia had required. Captain Newport freed Wingfield in early January, 1608, after arriving with the First Supply from England. Wingfieldy finaleft Jamestown three months later when Captain Newport returned to England.
The other prisoner did not get a trans-Atlantic trip home. George Kendall (a member of the council) was accused of being a spy for the Spanish at about the same time Wingfield was imprisoned on the Discovery, in mid-September 1607. The council removed Kendall and imprisoned him, and then had him executed.
Before Kendall became the first Virginia colonist to experience the death penalty, the colony had to manage two prisoners - but the colony had built no structure intended to serve just as a prison. The few early Jamestown structures that might have been sturdy enough to stop a prisoner from escaping were used to store food, gunpowder, muskets, and other essential supplies. Placing a prisoner next to valuables for a long time, and giving the prisoner nothing to do, was not a wise strategy...
It's not clear if more than one structure was converted into a de facto prison in 1607, but that seems likely. Keeping both Kendall and Wingfield together on the tiny Discovery would have been a problem, since the remaining members of the council would not have wanted two dispaced members to ally together and foment a counter-reaction. Kendall may have been kept in one of the storehouses that were erected inside the fort during the earliest stages of the settlement. In September 1607, when the colony discovered that prisoners required prisons, Jametown was still more of a camp than a city. Some colonial leaders were still living in tents.2