Charles's attempts in 1637 to impose an English style of worship on Scotland resulted in a rebellion, which in turn forced Charles to summon Parliament in 1640. This Parliament in turn used the crisis to take control of the government. It released political prisoners, arrested and executed Archbishop Laud and Sir Thomas Wentworth, Earl of Strafford, who they blamed for the king's policies. It also abolished the prerogative courts, limited the king's ability to raise taxes, and established that henceforth Parliament should meet every three years. On other measures, however, Parliament was hopelessly split. The division was further exacerbated by Charles's attempt to arrest some members of Parliament on charges of conspiracy. Failing that, the king withdrew with his supporters, known as Cavaliers. The Puritan remainder of Parliament, called Roundheads then issued a call to arms, and with Charles gathering his own forces, Civil war became inevitable.

The first Battle was fought at Edgehill in October 1642 resulted in a missed opportunity for Charles, and a drawn battle. The Roundheads eventually won the war, mainly because of the military leadership of Oliver Cromwell, who created the Ironsides cavalry regiment and then the New Model Army. Charles, who had surrendered to the Scots in 1646 was turned over to Cromwell in 1647, but managed to escape to reach a deal with the Scots, and attacked again in 1648. Once again he was defeated, and after being captured, was tried and executed in 1649. The "Rump" Parliament now abolished the monarchy and the House of Lords, and declared England a Commonwealth.

There was a taste of North Devon's Parliamentarian sympathies before the Civil War began. In the summer of 1640, 600 men of North Devon had been unwillingly conscripted to join a Royal Army being formed to march north against the Scots. On 11 July, a company passed through Tiverton on its way to Wellington, where it spent the night. The following day was a Sunday and some of the men noticed that on of their officers, a Lieutenant Evers, had not attended church. They at once suspected him of being a Catholic and angrily broke into his house, dragged him out, and murdered him in the street. The men then deserted and made their way back to their homes in North Devon, boasting of what they had done. Eventually a number of them were questioned or sought in connection with this crime. It had been established that nine came from Bishops Nympton and South Molton, while the remaining twelve came from the nearby parishes of Landkey, Chawleigh, West Anstey, Chittlehampton, Bishops Tawton, Oakford, Rackenford, Swimbridge and Witheridge.

In the light of this it is not surprising that, when two years later the Earl of Bath came to South Molton and attempted to publish the Royal Commission of Array (another form of conscription) he met with opposition. A threatening crowd of 1,000 people quickly gathered and sent him and his supporters packing. South Molton's hostility continued into 1644 and 1645. Much of the rural areas felt the same. Mark Stoyle has written:

As the war and its effects swung through North Devon and back again, villagers found themselves at the mercy of uncontrolled bands of horsemen on both sides. Cattle, sheep, poultry and crops were seized and the communities were left terrified. It is not surprising that a Witheridge resident tried to hide his money until the troubles were over. What happened next is described by William Chapple in his response for Witheridge to the Milles Inquiry of the 1750's, a questionnaire was sent to all Devon parishes:

There was a remarkable instance of the effects of a Damp in a well here in 1646. It seems the then troubles, which rendered property precarious, had induced one Walter Moore to hide a Bag of Money in this Well, which he fastened to a Pump-tree therein. After his death, some Persons, having information of hid treasure, opened the pit and one of them went down in search thereof. But, staying longer than expected, was followed by another, and he for the same reason by a third; none returning, a fourth person (one Thomas Molland) was let down by a rope, who, falling off the ladder, was drawn up half dead and with difficulty recovered. And, after having left the well sometime open to air, they got up the dead bodies of the other three, as well as ye money that they went in quest of, which, they privately divided among themselves. The Parish Register (which I have seen) mentions the burial of these three persons in one day (viz. John Greenslade, Robert Greenslade, and John Whitfield) and it was from thence that I knew the year when it happened, which however is not material, as the whole can only serve to caution people against endangering their lives in such circumstances.

By 1645, there was growing discontent against roving undisciplined groups, from either side, whose only purpose seemed to be theft and destruction. This led to the creation of bands of Clubmen, dedicated to defending their local parishes from marauders, whether Royalist or Parliamentarian. Clubmen were active in the Barnstaple and South Molton areas, particularly against Royalist thugs, nominally commanded by Lord Goring. So badly did these marauders behave that in Molland squire Courtney, a one-time supporter of the crown became leader of the Molland Clubmen. Events this near at hand may well have had an effect on Witheridge.

In 1643, John Radford became vicar of Witheridge, on the presentation of Robert Melhuish. For some reason he was presented again the following year, when he also became vicar of Puddington. He had been vicar at Thelbridge since 1632. In 1650, Robert Melhuish presented Hugh Shortrudge. We do not know what happened to Radford. Up to the 1640's, the Witheridge registers averaged about 25 entries a year. However, the Civil war seems to have had some effect, as entries became rather erratic. In 1642-43, the churchwardens failed to sign the registers. In 1644-45, there are only seven entries, and there are only two baptisms in September 1645, followed by the signatures of the wardens, one of which has been erased. There are no further entries until September 1646, from which date there are eight entries. There are no warden's signatures at the end of March 1647.