The year 1588 saw the country in great peril from the Spanish Armada, and soldiers were dispatched to Brentwood in readiness. Again in 1597 when Philip II, spurred by the sack of Cadiz by the Earl of Essex, threatened invasion, there was a muster of militia at Brentwood; 4,000 on foot and 400 on horseback were ordered to rendezvous at Ingatestone and Brentwood, but the Spanish threat came to nought. After 1600 the population was probably between six and seven hundred, living in some 90 houses, most of which were in the High Street and Back Street (now known as Hart Street).
The political and religious upheaval of the first half of the 17th century did not leave the town unmoved. Sir John Lucas of Shenfield, Sir Denner Strutt of Little Warley, Sir John Tyrell of East Horndon and Anthony Browne of South Weald all fought in support of the King, while Mr Luther of Kelvedon Hatch was prominent among the Parliamentarians.
However, the tide of war passed by until 1648, when the second Civil War broke out. The Royalists in Kent were defeated, marched into Essex via Bow Bridge and, after an overnight stop at Romford, marched through Brentwood on 8 June, where they were joined by a party on horse and foot under Sir Charles Lucas of Colchester. Close on their heels were the Parliamentarian forces of Colonel Whalley and Sir Thomas Fairfax, who eventually besieged the Royalists at Colchester and forced their surrender.
The troubled time came to an end in 1660 with the restoration of Charles II, when the bells were rung to celebrate at both South Weald and Brentwood. Samuel Pepys visited this town on a number of occasions, and celebrated the Coronation in Brentwood, where he awoke the following day the worse for drink.