In 1638, Baxter became master of the free grammar school at Dudley, where he commenced his ministry, having been ordained and licensed by John Thornborough, Bishop of Worcester. His success as a preacher was at first small; but he was soon transferred to Bridgnorth, in Shropshire, where, as assistant to a Mr Madstard, he established a reputation for vigorously discharging the duties of his office.

Baxter remained at Bridgnorth for nearly two years, during which time he took a special interest in the controversy relating to Nonconformity and the Church of England. He soon became alienated from the Church on several matters; and after the requirement of the "et cetera oath", he rejected episcopacy in its English form. He became a moderate Nonconformist; and continued as such throughout his life. Though regarded as a Presbyterian, he was not exclusively tied to Presbyterianism, and often seemed prepared to accept a modified Episcopalianism. He regarded all forms of church government as subservient to the true purposes of religion.

Kidderminster

One of the first measures of the Long Parliament was to reform the clergy; with this view, a committee was appointed to receive complaints against them. Among the complainants were the inhabitants of Kidderminster. The vicar George Dance agreed that he would give £60 a year, out of his income of £200, to a preacher who should be chosen by certain trustees. Baxter was invited to deliver a sermon before the people, and was unanimously elected as the minister of St Mary and All Saints' Church, Kidderminster. This happened in April 1641, when he was twenty-six.

His ministry continued, with many interruptions, for about 19 years; and during that time he accomplished many reforms in Kidderminster and the neighbourhood. He formed the ministers in the country around him into an association, uniting them irrespective of their differences as Presbyterians, Episcopalians and Independents. The Reformed Pastor was a book which Baxter published in relation to the general ministerial efforts he promoted.

The English Civil War

On the outbreak of the First English Civil War, Baxter blamed both parties and recommended the Protestation; but Worcestershire was a Royalist stronghold, and he was exposed to annoyance and danger in Kidderminster. He temporarily retired to Gloucester. On 23 October 1642, he was preaching at Alcester, during the Battle of Edgehill. He returned, only to be driven out again. He then moved to Coventry (a Parliamentary stronghold). There he found himself with no fewer than 30 fugitive ministers, among whom were Richard Vines, Anthony Burges, John Bryan and Obadiah Grew. He officiated each Sunday as chaplain to the garrison, preaching a sermon each to the soldiery, and the townspeople and strangers. Included among the congregants were Sir Richard Skeffington, Colonel Godfrey Bosvile, George Abbot the layman scholar, and others. After the Battle of Naseby he took the situation of chaplain to Colonel Edward Whalley's regiment, and continued to hold it till February 1647. During these stormy years he wrote his Aphorisms of Justification, which on its appearance in 1649, excited great controversy. Of numerous critics the one with whom Baxter engaged most closely was Christopher Cartwright.

Baxter's connexion with the Parliamentary army was a very characteristic one. He joined it that he might, if possible, contract the growth of sectaries in that field, and maintain the cause of constitutional government in opposition to republican tendencies of the time. He regretted that he had not previously accepted Oliver Cromwell's offer to become chaplain to the Ironsides. Cromwell avoided him; but Baxter, having to preach before him after he had assumed the Protectorship, chose for his subject the old topic of the divisions of the church, and in subsequent interviews argued with him about liberty of conscience, and even defended the monarchy he had subverted. This contact with Cromwell occurred when Baxter was summoned to London to assist in settling "the fundamentals of religion".

In 1647, Baxter was staying at the home of Lady Rouse, wife of Sir Thomas Rouse, 1st Baronet, of Rous Lench, Worcestershire. There, though debilitated by illness, he wrote the most of a major work, The Saints' Everlasting Rest (1650). During this period he was also an energetic campaigner for the establishment of a new University in Shrewsbury but lack of funding prevented success.

Return to Kidderminster

On his recovery he returned to Kidderminster, where he also became a prominent political leader. His sensitive conscience led him into conflict with almost all the contending parties in state and church. An all-day debate on 1 January 1650, with John Tombes at Bewdley was attended by about 1500 people on each side and ended in confused disorder.