Some of the middle colonies’ advantages proved to be challenges as well. The colonies of Pennsylvania, New York, New Jersey, and Delaware are notable for their religious diversity. Unlike continental Europe, people of various faiths, such as Quakers, Mennonites, Lutherans, Dutch Calvinists, and Presbyterians, lived in close proximity. The presence of so many religions made it impossible for just one faith to become dominant. This diversity led to greater religious tolerance than was seen in the firmly Puritan New England region, for example. However, this melting pot of religions also forced the middle colonies to confront the complexities of granting religious freedom to all.

Additionally, the advantage of having fertile farm land in the region bolstered the middle colonies’ economy. However, colonists had to meet the challenge of making the best use of the climate and land. The Northern part of the region, New York and New Jersey, was better suited to manufacturing because of the shorter growing season and cooler temperatures, while Pennsylvania and Delaware were better suited for farming. Thus, the middle colonies had to face the challenge of having a diversified economy.

Another problem was interaction with Native American tribes. At first, relations were friendly with the nearby Iroquois and Delaware tribes, who welcomed trade. However, colonists expanded westward as their population grew, encroaching upon Native American land. Later, during the French and Indian War, Native American tribes allied with the French against the British and attacked colonists throughout Pennsylvania.