Between 1639 and 1651 English overseas possessions were involved in the Wars of the Three Kingdoms, a series of civil wars and wars that were fought in and between England, Scotland and in Ireland.

Americas At the beginning of the war, fifty thousand Englishmen inhabited some twenty colonies in the Americas. Most of the colonies were founded in the decade prior to the start of the English Civil War (1642–1651) with the oldest existing being the Colony of Virginia (1607) and its offshoot, Bermuda (1609). The vast majority of the adult population were first generation settlers and thousands returned to the British Isles to fight or involve themselves in the politics of the Commonwealth of England (1649–1660).

Although the newer, Puritan settlements in North America, most notably Massachusetts, were dominated by Parliamentarians, the older colonies sided with the Crown. Starting with Bermuda, six colonies recognized Charles II after the regicide in 1649, including: Antigua, Barbados, Virginia, Maryland, and Newfoundland. The Parliamentarians were busy subduing Royalists in Scotland, Ireland, the Isles of Scilly, the Isle of Man, and the Channel Islands, and could not immediately force their rule on the colonies. The Virginia Company's settlements, Bermuda and Virginia (Bermuda's Independent Puritans were expelled, settling the Bahamas under William Sayle), as well as Antigua and Barbados were conspicuous in their loyalty to the Crown, and were singled out by the Rump Parliament in An Act for prohibiting Trade with the Barbadoes, Virginia, Bermuda and Antego, which was passed on 30 October 1650. This stated that the English Parliament, in order for "due punishment [to be] inflicted upon the said Delinquents",

The Act also authorised Parliamentary privateers to act against English vessels trading with the rebellious colonies: "All Ships that Trade with the Rebels may be surprized. Goods and tackle of such ships not to be embezeled, till judgement in the Admiralty.; Two or three of the Officers of every ship to be examined upon oath." A fleet was also assembled to take control of these colonies. By 1652, all were brought into line by the Commonwealth.

The new government introduced mercantilism with the first of the Navigation Acts in 1651. Soon the colonies became embroiled in the First Anglo-Dutch War (1652–1654) and the Anglo-Spanish War (1654–1660). By the Stuart Restoration, new colonies were added and the colonial population quadrupled to over two hundred thousand due to exiles, refugees, prisoners, and the Atlantic slave trade. In all the colonies that later became part of the United States, population growth throughout this period was vigorous, growing from a population of about 25,000 in 1640 to around 75,000 in 1660. The colonies also became more ethnically and religiously diverse. Another effect was the establishment of colonial assemblies in most of the colonies.

The Caribbean Barbados, the second most populous colony, experienced a division between Royalists and Parliamentarians during the civil war. The words "Roundhead" and "Cavalier" were banned to maintain peace. After the regicide, the Royalists gained control of the colonial assembly. Lord Willoughby was appointed Governor of Barbados, by Charles II in May 1650 and he banished the Roundheads. During this time he also sent a small colonizing party to Suriname, which established Fort Willoughby (now Paramaribo) in honour of the governor. The colony, now cut off from England, relied on trading with the Dutch Republic. This became the motivation for the Navigation Act 1651.

On 25 October 1651, a seven-ship force under Commodore George Ayscue arrived off Barbados, demanding that the island submit "for the use of the Parliament of England". Willoughby's reply (tellingly addressed to "His Majesty's ship Rainbow") was unyielding, declaring that he knew "no supreme authority over Englishmen but the King". With some 400 horsemen and 6,000 militia, he was prepared to resist any attempt at coercion.

Over the next month Barbados was blockaded. Dutch ships were seized, an act which would be one of the causes of the First Anglo-Dutch War. In early December, with the Royalist cause defeated in England, Ayscue began a series of raids against fortifications on the island and was reinforced by a group of thirteen ships bound for Virginia. On 17 December a force of more than 1,000 Barbadian militia was defeated by one of Ayscue's detachments. Governor Willoughby attempted to stem the spread of Parliamentary sympathies by hanging two of the returning militia soldiers and prohibiting the reading of documents from the blockading fleet. The Royalists held out for several more weeks until one of Willoughby's own commanders, Sir Thomas Modyford the assembly speaker, declared himself for Parliament. A battle was averted by a week of rain, after which Willoughby, perhaps having seen the hopelessness of his cause, sought negotiations. He was replaced as governor but Barbados and the Royalists there were not punished.

News of the fall of Barbados shocked the other Royalist colonies. Each of the other five soon capitulated without resistance, when Ayscue's fleet arrived to replace their governments. Following the conquest of Scotland and Ireland by the Commonwealth, Irish prisoners, and a smaller number of Scottish and English Royalists, were sent to the islands as indentured servants and became known as Redlegs.

In 1655, Cromwell sealed an alliance with the French against the Spanish. He sent a fleet to the West Indies under Admiral William Penn, with some 3,000 soldiers under the command of General Robert Venables, which was further reinforced in Barbados, Montserrat, St. Kitts and Nevis. Penn and Venables decided to lay siege to Santo Domingo but failed, because the Spanish had improved their defences in the face of Dutch attacks earlier in the century.

Weakened by fever, the English force then sailed west for Jamaica, the only place where the Spanish did not have new defensive works. In May 1655 they invaded at a place called Santiago de la Vega, now Spanish Town. They came, and they stayed, in the face of prolonged local resistance, reinforced by troops sent from New Spain in the Battle of Ocho Rios (1657) and the Battle of Rio Nuevo (1658). For England, Jamaica was to be the 'dagger pointed at the heart of the Spanish Empire' as it became a base for buccaneers. Cromwell, despite all difficulties, was determined that the presence should remain, sending reinforcements and supplies. Jamaica remained an English colony despite the exiled king's promise to return it to Spain in the event of his Restoration.

The Chesapeake Colonies and Bermuda Background The colonies of Virginia, Bermuda, and Maryland had strong Royalist sympathies, owing to their origins and demographics. Virginia, the oldest and third most populous colony, was turned into a crown colony in 1624 when the Royal charter of the Virginia Company was revoked. It was mostly high church Anglican in religion. Bermuda was originally an extension of Virginia and at the time was still administered by the Virginia Company's spin-off (or "under company"), the Somers Isles Company. Many Bermudians were Puritans, but the colony's Government and society were dominated by Royalists. After the independence of the colonies that were to form the United States, Bermuda would remain part of British North America. The much smaller Maryland was a proprietary colony founded by Roman Catholic gentry, supported by a Protestant underclass.

Bermuda, or the Somers Isles (originally named "Virginiola"), 640 miles from Cape Hatteras in North Carolina, had been settled in 1609 by the wreck of the Sea Venture and officially colonised as an extension of Virginia in 1612. Its administration had been transferred in 1615 to the Somers Isles Company, a spin-off of the Virginia Company, but it would retain close ties to Virginia until the American War of Independence. The Parliament of Bermuda (originally composed of a single house, the House of Assembly) was created in 1620. As virtually all of the land in Bermuda was owned by absentee landlords in England (the "Adventurers" of the Virginia and Somers Isles Companies), with most islanders being tenants or indentured servants, there was originally no property qualification to vote for the local assembly. This resulted in an Assembly that strongly reflected the interests of Bermudians, which became increasingly at odds with those of the Adventurers in England. Under the Virginia and Somers Isles Companies, the office of "Governor" was held by an absentee in London, with a "Lieutenant-Governor" (sometimes referred to as a "Deputy Governor") actually in Bermuda. When the first Lieutenant-Governor of Bermuda had been appointed by the Virginia Company in 1612 (in contrast to the company's earlier practice of dispatching governors to the colony, from the 1630s this office had been filled by a succession of prominent Bermudians), several other prominent settlers had been appointed to form an advisory privy council. With the establishment of an elected assembly, this became a legislative council, acting as both an upper house of the legislature and as a Cabinet (it is today the Senate of Bermuda). As all members of the council were ex-officio or appointed (with the Secretary of Bermuda as President), it was presumed to be more closely aligned with the interests of the Adventurers, but with those members having been appointed from the same emerging local elite class that provided candidates for election to the Assembly, it tended also to favour local interests.

Bermuda pioneered the cultivation of tobacco, but by the 1620s Virginia's tobacco industry was outproducing it and newer colonies were also adopting tobacco cultivation, driving down the profits the company earned from Bermudian tobacco. This resulted in many Adventurers selling their Bermudian land to the occupying tenants, creating a landed class in Bermuda who were technically Adventurers in the company, but who could not vote on its policies without attending its meetings in England in person. As the Bermudians attempted to redirect their colony to animal husbandry and food crops for local subsistence with the surplus increasingly exported to other colonies, they began building their own ships to deliver produce as they were otherwise reliant on the company's magazine ships (which served only to transport Bermuda's tobacco to the company in England and to return equipment and other goods for sale to Bermudians, in an attempt to give the company complete control of the economy and a profit on all imports as well as exports). The Adventurers in England, many of whom were Parliamentarians, exerted their authority to strangle Bermuda's emerging maritime industry, and the Bermudians' animosity towards the Adventurers in England consequently further acted to place them on the side of the Crown (the Somers Isles Company had tended towards the Royalist side in 1647, but was in the Parliamentary camp by 1649, and Robert Rich, 2nd Earl of Warwick, one of the major shareholders of the Somers Isles Company, was appointed Lord High Admiral of the Parliamentary navy from 1642 to 1649, and was related to Oliver Cromwell by the marriage of his grandson and heir to Cromwell's daughter). While Bermudians therefore tended towards the Royalist side, Bermuda largely escaped the effects of warfare.