Wars of the Three Kingdoms The Wars of the Three Kingdoms formed an intertwined series of conflicts that took place in England , Ireland , and Scotland between 1639 and 1651 after these three countries had come under the " Personal Rule " of the same monarch . The English Civil War has become the best - known of these conflicts and included the execution of the Three Kingdoms ' monarch , Charles I , by the English parliament in 1649 . The term , Wars of the Three Kingdoms , is often extended to include the uprisings and conflicts that continued through the 1650s until The English Restoration of the monarchy with Charles II , in 1660 ( from which point the Three Kingdoms were once again under a relatively peaceful personal union led by a Stuart monarch ) , and sometimes until Venner ' s Uprising the following year . The wars were the outcome of tensions between king and subjects over religious and civil issues . Religious disputes centred on whether religion was to be dictated by the monarch or the choice of the subject , the subjects often feeling that they ought to have a direct relationship with God unmediated by any monarch or human intermediary . The related civil questions were to what extent the king ' s rule was constrained by parliaments — in particular his right to raise taxes and armed forces without consent . Furthermore , the wars also had an element of national conflict , as Ireland and Scotland rebelled against England ' s primacy within the Three Kingdoms . The victory of the English Parliament — ultimately under Oliver Cromwell — over the King , the Irish and the Scots helped to determine the future of Great Britain as a constitutional monarchy with political power centred on London . The Wars of the Three Kingdoms also paralleled a number of similar conflicts at the same time in Europe — such as the Fronde in France and the rebellions of the Netherlands and Portugal against Spanish rule . The Wars included the Bishops ' Wars of 1639 and 1640 , the Scottish Civil War of 1644 – 45 ; the Irish Rebellion of 1641 , Confederate Ireland , 1642 – 49 and the Cromwellian conquest of Ireland in 1649 ( collectively the Eleven years war or Irish Confederate Wars ) ; and the First , Second and Third English Civil Wars of 1642 – 46 , 1648 – 49 and 1650 – 51 . Although the term is not new and was already used by James Heath in his book " A Brief Chronicle of all the Chief Actions so fatally Falling out in the three Kingdoms " , first published in 1662 , recent publications ' tendency to name these linked conflicts the " Wars of the Three Kingdoms " represents a trend by historians aiming to take a unified overview rather than treating some of the conflicts as mere background to the " English Civil War " . Some , such as Carlton , Gaunt and Royal have labelled them the British Civil Wars , but this can be misleading , because although the three realms were linked by a personal union , the three kingdoms did not become a single political entity until the Act of Union 1800 . Background . The personal union of the three kingdoms under one monarch came about as a relatively recent development in contemporary 17th - century terms . Since 1541 , monarchs of England had also styled their Irish territory as a Kingdom ( ruled with the assistance of a separate Irish Parliament ) , while Wales became more closely integrated into the Kingdom of England under Henry VIII . Scotland , the third separate kingdom , was governed by the House of Stewart , and the three kingdoms were united under the same monarch when King James VI of Scotland succeeded Elizabeth to the English throne in 1603 . Ruling over these three diverse kingdoms proved difficult for James and his successor Charles I of England , particularly when they tried to impose religious uniformity on the three kingdoms . Different religious conditions pertained in each of these jurisdictions . With the English Reformation , King Henry VIII made himself head of the Protestant Church of England and outlawed Catholicism in England and Wales . In the course of the 16th century Protestantism became intimately associated with national identity in England : English folk in general saw Catholicism as the national enemy , especially as embodied in France and Spain . However , Catholicism remained the religion of most people in Ireland and was for many a symbol of native resistance to the Tudor conquest of Ireland in the 16th century . In the Kingdom of Scotland the Protestant Reformation was a popular movement led by John Knox . The Scottish Parliament legislated for a National Presbyterian church , the presbyterian Church of Scotland or " Kirk " , and the Catholic Mary , Queen of Scots , was forced to abdicate in favour of her son James VI of Scotland . He grew up under a regency disputed between Catholic and Protestant factions , then took power and aspired to be a " universal King " favouring the English Episcopalian system of bishops appointed by the king . In 1584 , he introduced bishops , but met vigorous opposition and had to concede that the General Assembly running the church should continue to do so . Calvinists reacted against the formal liturgy of " the Book of Common Order " moving increasingly to extempore prayer , though this was opposed by an Episcopalian faction . Religious confrontation in Scotland . James VI remained Protestant , taking care to maintain his hopes of succession to the English throne . He duly also became James I of England in 1603 and moved to London . His diplomatic and political skills now concentrated fully in dealing with the English Court and Parliament at the same time as running Scotland by writing to the Privy Council of Scotland and controlling the Parliament of Scotland through the Lords of the Articles . He stopped the Scottish General Assembly from meeting , then increased the number of Scottish bishops , and in 1618 , held a General Assembly and pushed through " Five Articles " of Episcopalian practices which were widely boycotted . In 1625 , he was succeeded by his son Charles I who was less skilful or restrained and was crowned in St Giles Cathedral , Edinburgh , in 1633 with full Anglican rites . Opposition to his attempts to enforce Anglican practices reached a flashpoint when he introduced a Book of Common Prayer . Charles ' confrontation with the Scots came to a head in 1639 , when Charles tried and failed to coerce Scotland by military means . England . Charles shared his father ' s belief in the Divine Right of Kings , and his assertion of this led to a serious breach between the Crown and the English Parliament . While the Church of England remained dominant , a powerful Puritan minority , represented by around one third of the members of Parliament , had much in common with the Presbyterian Scots . The English Parliament also had repeated disputes with the King over such subjects as taxation , military expenditure and the role of parliament in government . While James I had held the same opinions as his son with regard to royal prerogatives , he had enough charisma to persuade the Parliament to accept his policies . Charles did not have this skill in human management and so , when faced with a crisis in 1639 – 42 , he failed to prevent his Kingdoms from sliding into civil war . When Charles approached the Parliament to pay for a campaign against the Scots , they refused , declared themselves to be permanently in session and put forward a long list of civil and religious grievances that Charles would have to remedy before they approved any new legislation . Ireland . Meanwhile , in the Kingdom of Ireland ( proclaimed such in 1541 but only fully conquered for the Crown in 1603 ) , tensions had also begun to mount . Charles I ' s Lord Deputy there , Thomas Wentworth , had antagonised the native Irish Catholics by repeated initiatives to confiscate their lands and grant them to English colonists . He had also angered Roman Catholics by enforcing new taxes but denying them full rights as subjects . This situation became explosive in 1639 when Wentworth offered the Irish Catholics the reforms they had desired in return for them raising and paying for an Irish army to put down the Scottish rebellion . Although plans called for an army with Protestant officers , the idea of an Irish Catholic army enforcing what many saw as tyrannical government horrified both the Scottish and the English Parliaments , who in response threatened to invade Ireland . War . Modern historians have emphasised the lack of the inevitability of the Civil Wars , pointing out that all sides resorted to violence in a situation marked by mutual distrust and paranoia . Charles ' initial failure to bring the Bishops ' Wars to a quick end also made other discontented groups feel that force could serve to get what they wanted . Alienated by English / Protestant domination and frightened by the rhetoric of the English and Scottish Parliaments , a small group of Irish conspirators launched the Irish Rebellion of 1641 , ostensibly in support of the " King ' s Rights " . The rising featured widespread assaults on the Protestant communities in Ireland , sometimes culminating in massacres . Rumours spread in England and Scotland that the killings had the King ' s sanction and that this foreshadowed their own fate if the Kings ' Irish troops landed in Britain . As a result , the English Parliament refused to pay for a royal army to put down the rebellion in Ireland and instead raised their own armed forces . The King did likewise , rallying those Royalists ( some of them members of Parliament ) who believed that loyalty to the Legitimate King outweighed other important political principles . The English Civil War broke out in 1642 . The Scottish Covenanters , as the Presbyterians called themselves , sided with the English Parliament , joined the war in 1643 , and played a major role in the English Parliamentary victory . The King ' s forces found themselves ground down by the efficiency of Parliament ' s New Model Army — backed by the financial muscle of the City of London . Charles I surrendered to the Scottish army at encamped at Southwell besieging Newark - on - Trent on 5 May 1646 . What remained of the English and Welsh Royalist armies and garrisons surrendered piecemeal over the next few months . In Ireland , the rebel Irish Catholics formed their own government — Confederate Ireland — with the intention of helping the Royalists in return for religious toleration and political autonomy . Troops from England and Scotland fought in Ireland , and Irish Confederate troops mounted an expedition to Scotland in 1644 , sparking the Scottish Civil War . In Scotland , the Royalists had a series of victories in 1644 – 45 , but were crushed with the end of the first English Civil War and the return of the main Covenanter armies to Scotland . Charles I was handed over by the Scots to the English when the returned to Scotland as part of the conditions for the English Parliament paying the Scots a large sum of money to help pay for the cost of their English campaign . From his surrender until the outbreak of the Second Civil war the Scots , the Presbyterian in the English Parliament and the " Grandee s " of the New Model Army all negotiated Charles and with each other trying to reach an accommodation . The breach between the New Model Army and Parliament widened day by day until finally the Presbyterian party , combined with the Scots and the remaining Royalists , felt itself strong enough to begin a Second English Civil War . The New Model Army vanquished English Royalists , their Scottish Engager s allies . Not being able to reconcile themselves with King or the Presbyterian majority in Parliament , the " Grandees " and their civilian supporters used soldiers under the command of Colonel Pride to purge the English Parliament of those who opposed their polices . The Rump of the Long Parliament then passed enabling legislation for the trial of Charles I , who was found guilty of treason against the English commons and was executed on 30 January 1649 . After the execution of King Charles I the Rump Parliament passed a series of acts making England a republic with the House of Commons ( sitting without the House of Lords ) the legislative and a Council of State as the executive . In the other two Kingdoms the execution of King Charles I caused the warring parties in those two kingdoms to unite and recognise Charles II as king of Great Britain , France and Ireland . To deal with the threat that the two kingdom posed to the English Commonwealth , the Rump Parliament sent a parliamentary army under Cromwell to invade subdue Ireland . Cromwell and his army proceeded to do this . At the end of May 1650 Cromwell left Ireland ( leaving the English army in Ireland to continue the conquest ) and returned to England to take command of an English army which shortly afterwards invaded Scotland It beating a Covenanter army at the Battle of Dunbar ( 1650 ) 3 September 1650 . His army then proceeded to occupy Edinburgh and the rest of Scotland south of the Forth . When in Cromwell advanced with the bulk of his army over the Forth towards Stirling a Scottish Royalist army under the command of Charles II stole the march on Cromwell and invaded England . Cromwell divided his army , leaving some in Scotland to continue the conquest and led the rest south in pursuit . The Royalist army failed to gather much support from English Royalists , so instead of heading straight for London and certain defeat , Charles went to Worcester in the hope that the West of England and Wales would rise up against the Commonwealth . This did not happen and a year to the day since the battle of Dunbar the New Model Army with support from English militia regiments won the Battle of Worcester vanquishing a predominately Scottish Royalist army . This was the last and most decisive victory in the Wars of the Three Kingdoms . Aftermath . Following the defeat of all the opponents of the English Parliamentary New Model Army , the " Grandees " of the Army and their civilian supporters dominated the politics of all three nations for the next nine years ( see Interregnum ( 1649 – 1660 ) ) . The Rump Parliament had decreed that England was a Commonwealth , and although Ireland and Scotland were ruled by military governors , representatives of constituencies in Ireland and Scotland sat in the English parliaments of the Protectorate . With the death of the Lord Protector Oliver Cromwell in 1658 , the Commonwealth fell into a period of instability . It ended in 1660 when the English army occupying Scotland marched south under the command of General George Monck , seized control of London , and , with the agreement of the English civilian establishment , invited Charles II to return to the Three Kingdoms as king ( an event known as the Restoration ) . While the Wars of the Three Kingdoms pre - figured many of the changes that would shape modern Britain , in the short term they resolved little . The English Commonwealth did achieve a compromise ( though a relatively unstable one ) between a monarchy and a republic . In practice , Oliver Cromwell exercised political power because of his control over the Parliament ' s military forces , but his legal position remained unclear , even when he became Lord Protector . None of the several proposed constitutions ever came into effect . Thus the Commonwealth and the Protectorate established by the victorious Parliamentarians left little behind it in the way of new forms of government . Two important legacies remain from this period : English Protestants experienced religious freedom during the Interregnum , but not English Roman Catholics . The new authorities abolished the Church of England and the House of Lords . Cromwell dismissed the Rump Parliament and failed to create an acceptable alternative . Nor did Cromwell and his supporters move in the direction of a popular democracy , as the more radical fringes of the Parliamentarians ( such as the Levellers ) wanted . The New Model Army occupied Ireland and Scotland during the Interregnum . In Ireland , the new government confiscated almost all lands belonging to Irish Catholics as punishment for the rebellion of 1641 ; harsh Penal Laws also restricted this community . Thousands of Parliamentarian soldiers settled in Ireland on confiscated lands . The Commonwealth abolished the Parliaments of Ireland and Scotland . In theory , these countries had representation in the English Parliament , but since this body never received real powers , such representation remained ineffective . When Cromwell died in 1658 the Commonwealth fell apart without major violence , and Charles II returned as King of England , Scotland and Ireland in 1660 . Under the English Restoration , the political system returned to the constitutional position of before the wars . The new régime executed or imprisoned for life those responsible for the regicide of Charles I . Neo - Royalists dug up Cromwell ' s corpse and gave it a posthumous execution . Religious and political radicals held responsible for the wars suffered harsh repression . Scotland and Ireland regained their Parliaments , some Irish retrieved confiscated lands , and the New Model Army disbanded . However , the issues that had caused the wars — religion , the power of Parliament and the relationship between the three kingdoms — remained unresolved , only postponed to re - emerge as matters fought over again in the Glorious Revolution of 1688 . Only after this point did the features of modern Britain seen in the Civil Wars emerge permanently : a Protestant constitutional monarchy with England dominant , and a strong standing army .