The seventeenth century would prove to be a momentous and turbulent century in the history of both Cork city and Ireland. It saw the re-establishment of the power of the crown over Ireland; a power that was now aligned with the Protestantism of the Reformation. It also witnessed the beginnings of the decline of the old Gaelic civilisation. Most historians regard the defeat of the Irish and Spanish forces at the Battle of Kinsale in 1601 and the flight of the earls in 1607 as watersheds in the history of Ireland.
At the beginning of the seventeenth century, the merchant families who controlled the civic government of Cork city were again firmly Roman Catholic, and inspired by priests who returned from the Counter Reformation seminaries of Europe. The merchants and many of the citizenry resented the English garrison in the city and the practice of quartering troops, sent to fight in the Elizabethan wars, with the citizens. Surviving records from this period contain complaints from the civic authorities in Cork about this practice. The English authorities regarded the merchant oligarchy with suspicion due to its Catholicism and it was thought to be in league with Gaelic and Catholic forces outside the city. The letters of William Lyon, Protestant Bishop of Cork during this period, warn the English authorities to be wary of their Cork subjects. An early symptom of this tension was the so-called 'Recusant Revolt' of 1603. On the death of Queen Elizabeth I, the leading Catholic families in Cork refused to proclaim James I as king and, for a short time, the Catholic mass and liturgy were restored to the churches in the city. Lord Mountjoy soon put down the revolt, which was mirrored in other Irish cities.
While the civic governement of the city remained in the hands of the merchant patriciate, the tensions between it and the officials of the crown continued to simmer. Members of the leading Catholic families, Meades, Tirrys, Goolds and others were fined for non-attendance at formal religious ceremonies conducted according to the Anglican rite. The charter of 1608, while it created the County of the City of Cork, which covered a much larger area than the old medieval walled city and adjoining suburbs, also retained for the crown the right to poundage, tonnage and customs in the Port of Cork. This was a severe financial blow to the merchants of the city.
Matters came to a head in 1644, following the 1641 rebellion. In that year it was discovered that some of the leading citizens of Cork had been conspiring with Lord Muskerry, a military commander loyal to the Catholic Confederacy. On learning of this, Lord Inchiquin took extreme action. On 26 June 1644, he decreed the expulsion of the Irish and Catholic population of Cork from the city. The power of the Old Catholic merchant families, which had dominated the civic life of Cork for centuries, was broken.
Despite the political turbulence, the economic fortunes of Cork began to improve in the first half of the seventeenth century, after two centuries of relative decline. Historians and geographers using evidence from maps, surveys, and other sources estimate that the population of the city may have trebled from approximately 3,000 in the year 1600 to approximately 9,000 in 1640. The number of streets, lanes, and buildings within the old walled city increased, and similar developments took place in the suburbs.
The English government encouraged trade and the development of agriculture by granting patents for the holding of markets and fairs. Trade was also stimulated by improvement in the infrastructure for transport and communications with the opening of new roads, the felling of woods and the building of fortified houses. Cork became a major centre for the import and export of goods. The export of hides, pipestaves, rugs and tallow increased. Among imported goods were wine, salt and other commodities. Trade with Bristol was especially important and trade with European ports, for example Bordeaux, began to flourish. This period also saw the beginnings of trade with the West Indies and some historians have discerned the tentative beginning of the butter trade, a development that would assume enormous importance in the later economic history of Cork.