Apart from the British seas, Charles's main initiative to bring uniformity to his kingdoms was a new book of common prayer. Introduced in Scotland in 1637, it caused widespread and deep anger. A collective repudiation, the National Covenant, emerged on 28 February 1638; it included an oath and band committing Scots to the shape of the kirk being formed by free assemblies and the estates. Although alongside the defence of the true religion it talked of the defence of the king's authority within its established limits, Charles perceived the covenant as an assault on his authority. Regardless of the constitutional forms and privileges of individual territories, all kings understood obedience to be the obligation of their subjects, and composite monarchy offered Charles the means to reimpose royal authority, by drawing upon English and Irish forces. The Covenanters do not seem to have initially considered this possibility, expecting that by presenting a more or less united Scotland, as demonstrated by the broad base of subscriptions to the covenant, Charles would be rendered pliable. They quickly realised their mistake, as the royal navy sailed into the Firth of Forth and an army mustered south of the border. The navy failed to reimpose royal authority in the two Bishops’ Wars of 1639 and 1640, but it was not as ineffective as sometimes supposed and loomed over the covenanted regime's negotiations through the 1640s, as their search for confessional and political security through union rested on the unstated assumption that security could not be permanently assured through arms alone, because they had no reply to naval threats.

The covenanted regime conjured successive large armies for deployments in all three Stuart kingdoms through the 1640s, fielding up to 30,000 men. This was a Scottish military revolution, and the quest to support these forces did, for a time, bring about a transformation in Scottish fiscal capacity. However, it was not accompanied by similar improvements in naval capacity. This lack has been noted by historians, as has the limited success of Scottish privateers in these years. Laura Stewart says that the Scots had no incentive to develop naval forces because their military policy was predicated upon making England pay for the Scottish war machine.