After the defeat at Naseby in 1645, surviving elements of the Royalist army were scattered throughout the region. Charles I retreated to Newark Castle with a body of men, but then tried to travel north to meet up with a Scottish army. His passage was blocked by Parliamentarian forces, and he retreated southwards to Stamford. On 24 August, Charles headed south towards Huntingdon. The reported number of his force varies from 4000 cavalry to 500 combined cavalry and dragoons.
On 23 August, a Parliamentarian force of 400 dragoons were based near Stilton and moved to intercept Charles. Somewhere between Stilton and Huntingdon, Royalist cavalry attacked this force, who were new recruits, driving them back towards Huntingdon. The defences on the north side of the town were inadequate and the Royalists entered the town. The Parliamentarian force was scattered, killed or captured.
The people of Huntingdon welcomed the king, who set up court at the George Inn. The Royalists stayed until the 26 August, extracting provisions and money from the town. The Eastern Association, fearful that the next attack would be on Cambridge itself, mobilised more troops to meet the threat, but were unable to act before the Royalists left, taking hostages with them.
The scale of the action is disputed and although it is traditionally believed that the Battle of Huntingdon was responsible for much damage done to the town, including the destruction of the churches of St Benet and St John on the High Street. However, others have pointed out that the numbers involved were relatively small, and most of the action appears to have taken place outside the town on the road towards Stilton. Once the minimal defences were seized, Huntingdon's defenders appear to have been driven off, so the scale of action that took place within the town may have been minimal, and the destruction of the churches more the result of inadequate maintenance and funds than hostile action. Parliamentarian propaganda made much of the Royalist soldiers causing chaos in the town and mistreating the population during their stay.