The authority of the new provisional government was soon challenged by the , councils of representatives from the workers and .

from the religious point of view, the conflicts began because of the enmity between catholic and protestants. in 1649, at the insistence of baltimore, the colonial assembly approved the act of religious tolerance, the first law in the colonies granting freedom of worship, though only for christians. in 1654, however, with the protestants of maryland in the majority, the act was revoked. the almost civil war broke out and order was not restored until 1658, when lord baltimore was returned to power.

on the issue of class conflict, the chesapeake region offered few economic opportunities to contract employees who had served their term of obligation. even with the small amount of capital needed to grow tobacco, former hired servants at best became subsistence farmers, a mature class for those called to rebellion, such as those proposed by nathaniel bacon. as the number of new hired workers declined because of limited chances of progress and reports of severe treatment, they were replaced by african slaves.

from the racial point of view, after 1660, the chesapeake colonies imposed laws that defined slavery as a lifelong and hereditary condition based on race. this made slaves profitable because planters could rely not only on their work but also on their children. the slave population, which numbered four thousand in virginia and maryland in 1675, grew significantly by the end of the century.