Civil unrest was building up in the 16th century, for rising prices, and the decline in Suffolk of the all important cloth industry led to considerable discontent among the town and country workers. This unrest escalated into a serious rebellion which broke out in Norfolk during Edward VI's reign in1549. It was based on the sudden increase in poverty and the extension of enclosures of land by the big landowners, causing the villagers loss of common grazing land. The Spanish Ambassador wrote 'They have risen in every part of England asking for things just and unjust'.

The rebels were led by Robed Kett, a tanner and small landowner, and they set up camps at Bury St Edmunds, Melton (near Woodbridge), and just outside Norwich. They stormed the city with Kett leading a force of 16,000 insurgents, and defeating 1200 Crown troops, they captured it. John Dudley, the Earl of Warwick was sent with a new army of 12,000 men to recapture Norwich and with a battle fought on St Andrews Plain, the rebels were defeated and some 3000 men died. Kett was tried in London, condemned and brought back to Norwich to be hanged on the Castle Walls.

Trouble on a national scale was on the horizon with the war with Spain.

Following a tour of East Anglia, earthworks were raised at Lowestoft and Gorleston, a battery of 12 guns set up at Aldeburgh and another battery of cannons at Gun hill, Southwold. In March 1580, Suffolk towns were ordered to provide ships for the coming emergency. Ipswich and Harwich sent jointly two ships and a pinnace (smaller ship), Lowestoft the 'Matthew' which was returned as 'not worth keeping', and Aldeburgh's 'Marygold' was sent back as it had not been provisioned. 2000 Suffolk men reported to the Tilbury Camp (Essex) in August 1588 in time to hear Elizabeth's speech, but with the news of the defeat by Drake and other captains of the Spanish Armada, the Suffolk contingent quite thankfully returned swiftly home.

With the death of Queen Elizabeth in 1603, James VI of Scotland was crowned as James I of England, and during his reign experienced the well known Gunpowder Plot. He was succeeded by his son as Charles I in 1615, who was soon inflicting taxes on the population in order to raise money for different purposes. The most hated was the 'Ship Tax' which fell so heavily on the maritime counties. Norwich had to find the money to provide a ship of 800 tons and 200 seamen, Essex a ship of 700 tons and Yarmouth had to find £940. Colchester, MaIdon and Harwich had to raise £6,615 and Suffolk an annual assessment of £8,000. These were some of many grievance and in 1639 a group of soldiers mutinied at Bungay, and this extended to Beccles, where the mutineering soldiers played games with the residents. A mock court was set up and there were 'many pranks they played which are not fit to be written'.

In Parliament, Oliver Cromwell supported his cousin from Buckinghamshire, John Hampden, in refusing the pay the Ship Tax, and when Charles raised his standard at Nottingham in 1642, the Civil War had begun. An Eastern Association of Counties was formed, which included Suffolk, and Cromwell was commissioned to raise cavalry and an armed force which, as East Anglia was mainly for Parliament, would be used to fight the King and his army.