In many New England communities a majority in the churches of the standing order bitterly opposed the new evangelism, and those who came under its influence felt constrained to organize "Separate" or "New Light" churches. These were severely persecuted by the dominant party and were denied even the scanty privileges that Baptists had succeeded in gaining. As the chief objection of the "Separates" to the churches of the standing order was their refusal to insist on personal regeneration as a term of membership, many of them were led to feel that they were inconsistent in requiring regenerate membership and yet administering baptism to unconscious infants. In several cases entire "Separate" churches reached the conviction that the baptism of infants was not only without Scriptural warrant but was a chief corner-stone of state-churchism, and transformed themselves into Baptist churches. In many cases a division of sentiment came to prevail on the matter of infant-baptism, and for a while mutual toleration prevailed; but mixed churches had their manifest disadvantages and separation ultimately ensued.

Among the Baptist leaders gained from Congregationalism as a result of the awakening was Isaac Backus (1724-1806), who became the New England champion in the cause of religious liberty and equality, and the historian of his denomination. To Daniel Marshall (d. 1784) and Shubael Stearns, "New Light" evangelists who became Baptists, the spread of Baptist principles and the multiplication of Baptist churches throughout the southern colonies were in great measure due. The feeble Baptist cause in Virginia and North Carolina had been considerably strengthened by missionaries from the churches of the Philadelphia Association, including Benjamin Griffith, John Gano (1727-1804), John Thomas, Benjamin Miller, Samuel Eaton, John Garrard and David Thomas, and several churches, formed or reformed under their influence, united with the association. In 1776 the Ketockton Association was formed by this group of churches. The Virginia colonial government, in earlier days cruelly intolerant, gave a limited toleration to Baptists of this type; but the "Separate" Baptists were too enthusiastic and too much alive to the evils of state control in religious matters to be willing to take out licences for their meetings, and soon came into sharp conflict with the authorities.

Stearns was an evangelist of great power. With Marshall, his brother-in-law, and about a dozen fellow-believers he settled at Sandy Creek, North Carolina, and in a few years had built up a church with a membership of more than six hundred. Marshall afterward organized and ministered to a church at Abbott's Creek about 30 m. distant. From these centres "Separate" Baptist influence spread throughout North and South Carolina and across the Georgia border, Marshall himself finally settling and forming a church at Kiokee, Georgia. From North Carolina as a centre "Separate" Baptist influence permeated Virginia and extended into Kentucky and Tennessee. The Sandy Creek Association came to embrace churches in several colonies, and Stearns, desirous of preserving the harmonious working of the churches that recognized his leadership, resisted with vehemence all proposals for the formation of other associations.

From 1760 to 1770 the growth of the "Separate" Baptist body in Virginia and the Carolinas was phenomenal. Evangelists like Samuel Harris (1724-c.1794) and John Waller (1741-1802) stirred whole communities and established Baptist churches where the Baptist name had hitherto been unknown. The Sandy Creek Association, with Stearns as leader, undertook to "unfellowship ordinations, ministers and churches that acted independently," and provoked such opposition that a division of the association became necessary. The General Association of Virginia and the Congaree Association of South Carolina now took their places side by side with the Sandy Creek. The Virginia "Separate" Baptists had more than doubled their numbers in the two years from May 1771 to May 1773. In 1774 some of the Virginia brethren became convinced that the apostolic office was meant to be perpetuated and induced the association to appoint an apostle. Samuel Harris was the unanimous choice and was solemnly ordained. Waller and Elijah Craig (1743-1800) were made apostles soon afterward for the northern district. This arrangement, soon abandoned, was no doubt suggested by Methodist superintendency. In 1775 Methodist influence appeared in the contention of two of the apostles and Jeremiah Walker for universal redemption.

Schism was narrowly averted by conciliatory statements on both sides. As a means of preserving harmony the Philadelphia Confession of Faith, a Calvinistic document, with provision against too rigid a construction, was adopted and a step was thus taken toward harmonizing with the "Regular" Baptists of the Philadelphia type. When the General Association was sub-divided (1783), a General Committee, made up of delegates from each district association, was constituted to consider matters that might be for the good of the whole society. Its chief work was to continue the agitation in which for some years the body had been successfully engaged in favour of religious equality and the entire separation of church and state. Since 1780 the "Separate" Baptists had had the hearty co-operation of the "Regular" Baptists in their struggle for religious liberty and equality. In 1787 the two bodies united and agreed to drop the names "Separate" and "Regular." The success of the Baptists of Virginia in securing step by step the abolition of everything that savoured of religious oppression, involving at last the disestablishment and the disendowment of the Episcopal Church, was due in part to the fact that Virginia Baptists were among the foremost advocates of American independence, while the Episcopal clergy were loyalists and had made themselves obnoxious to the people by using the authority of Great Britain in extorting their tithes from unwilling parishioners, and that they secured the co-operation of free-thinking statesmen like Thomas Jefferson and James Madison and, in most measures, that of the Presbyterians.

The Baptist cause in New England that had profited so largely from the Great Awakening failed to reap a like harvest from the War of Independence. The standing order in New England represented the patriotic and popular party. Baptists lost favour by threatening to appeal to England for a redress of their grievances at the very time when resistance to English oppression was being determined upon. The result was slowness of growth and failure to secure religious liberty. Though a large proportion of the New England Baptists co-operated heartily in the cause of independence, the denomination failed to win the popularity that comes from successful leadership.

About 1762 the Philadelphia Association began to plan for the establishment of a Baptist institution of learning that should serve the entire denomination. Rhode Island was finally fixed upon, partly as the abode of religious liberty and because of its intelligent, influential and relatively wealthy Baptist constituency, the consequent likelihood of procuring a charter from its legislature, and the probability that the co-operation of other denominations in an institution under Baptist control would be available. James Manning (1738-1791), who had just been graduated from Princeton with high honours, was thought of as a suitable leader in the enterprise, and was sent to Rhode Island (1763) to confer with leading men, Baptist and other. As a result a charter was granted by the legislature in 1764, and after a few years of preliminary work at Warren (where the first degrees ever bestowed by a Baptist institution were conferred in 1769), Providence was chosen as the home of the college (1770). Here, with Manning as president and Hezekiah Smith (1737-1805), his class-mate at Princeton, as financial agent and influential supporter, the institution (since 1804 known as Brown University) was for many years the only degree-conferring institution controlled by Baptists. The Warren Association (1767) was organized under the influence of Manning and Smith on the model of the Philadelphia, and became a chief agency for the consolidation of denominational life, the promotion of denominational education and the securing of religious liberty.

Hezekiah Smith was a highly successful evangelist, and through his labours scores of churches were constituted in New England. As chaplain in the American Revolutionary Army he also exerted a widespread influence.

The First Church, Charleston, which had become almost extinct through Arminianism in 1746, entered upon a career of remarkable prosperity in 1749 under the leadership of Oliver Hart (1723-1795), formerly of the Philadelphia Association. In 1751 the Charleston Association was formed, also on the model of the Philadelphia, and proved an element of denominational strength. The association raised funds for domestic missionary work (1755 onward) and for the education of ministers (1756 onward). Brown University shared largely in the liberality of members of this highly-cultivated and progressive body. Among the beneficiaries of the education fund was Samuel Stillman (1737-1807), afterward the honoured pastor of the Boston church. The most noted leader of the Baptists of South Carolina during the four decades following the War of Independence was Richard Furman (1755-1825), pastor of the First Church, Charleston. The remarkable numerical progress of Baptists in South Carolina from 1787 to 1812 (from 1620 members to 11,325) was due to the "Separate" Baptist movement under Stearns and Marshall far more than to the activity of the churches of the Charleston Association. Both these types of Baptist life permeated Georgia, the latter making its influence felt in Savannah, Augusta and the more cultivated communities, the former evangelizing the masses.

Many negro slaves became Baptists in Virginia, the Carolinas and Georgia. In most cases they became members of the churches of the white Baptists; but in Richmond, Savannah and some other towns they were encouraged to have churches of their own.

By 1812 there were in the United States 173,972 Baptist church members, the denominational numerical strength having considerably more than doubled since the beginning of the 19th century.