Three years after his first wife died Penn married again, this time Hannah Callowhill, of Bristol. Soon afterward he lost his oldest child, Springett, a boy of great charm and a close companion of his father. Of Guli Penn's two other children, William became dissipated and was a great disappointment to Penn, and Letitia married William Aubrey, who turned out to be a very disagreeable son-in-law. By his second wife Penn had six children, four of whom, John, Thomas, Margaret, and Richard, ultimately became the joint owners of Pennsylvania.

Penn now moved to the English city of Bristol, where he continued making plans for his province, and preaching and arguing with people who did not approve of his religion. The Quakers were then doing a certain amount of missionary work, and the story goes that Penn sought out a young Russian prince who was studying shipbuilding in England, and gave him Quaker books which he explained to him. In time this prince became the Emperor Peter the Great of Russia, and he is said always to have taken great interest in the Quakers because of what Penn had taught him.

Meantime, much had happened in Pennsylvania. The history of the province had been full of ups and downs, many of its difficulties being due to the fact that for fifteen years Penn had been obliged to stay away from it. There had been many squabbles between the settlers and the men appointed to govern the province, but in spite of disagreements the colony had grown until now there were nearly twenty thousand settlers there.

When Penn left his colony in 1684, he had placed the power in the charge of a Council of eighteen men, and each of the eighteen had felt that it was his duty to do all the governing. When he learned that this system did not work well, Penn had tried to mend matters by doing away with the Council and appointing five commissioners. But this did not work very well, either, and in less than a year Penn appointed an old soldier of Cromwell's army, Captain John Blackwell, to replace the commissioners, and act as a deputy governor. The Quakers, however, did not like being in charge of a soldier, and made matters so difficult for Captain Blackwell that he resigned his post. Then followed another Council, and then another deputy governor, so that in ten years the form of government was changed no less than six times.

When William III. took the province away from Penn, he appointed a captain general, Colonel Benjamin Fletcher, who served until the colony was given back to Penn, a year and ten months later. Then Penn appointed his cousin, Markham, to be deputy governor, with two assistants. Markham, although he had a troubled time of it, managed to keep charge until William Penn was able to join him in 1699. All this time Penn had been paying salaries and spending money on his home at Pennsbury, and had been receiving nothing in return.

There was another reason for Penn's returning to his colony as soon as he could, and that was that King William was growing impatient at the stories he heard of the misgovernment of Pennsylvania, and was determined that something should be done to put things on a more stable footing. So, under the urging of friends at court who knew the king's mind, Penn collected what money he could, and on September 9, 1699, embarked with his wife and his daughter Letitia on the ship Canterbury at Southampton. The voyage was long and stormy, but three months later—toward the end of November—the ship reached the mouth of the Delaware River. The ship was so slow in sailing up the river that when New Castle was reached, Penn left her and was rowed to Chester.

Many settlers, hearing of the arrival of the proprietor of the province, flocked to Chester to greet him. Among them was a Quaker who had been well known in England, Thomas Story, who had traveled extensively in America. Penn and Story spent the night together at the house of Lydia Wade, near Chester, and Story told the proprietor all that had been happening in the province, including the scourge of yellow fever, or "Barbadoes distemper," as it was often called, that had visited Philadelphia a short time before and proved fatal to more than two hundred people.

Next day Penn returned to the Canterbury and sailed on up to Philadelphia. Here he landed, paid a short visit to Markham, the deputy governor, and then went to the Quaker meetinghouse, where he preached to a great congregation.

He brought with him to Philadelphia a young man named James Logan, who acted as his secretary; in time Logan became Penn's chief representative, and one of the wisest of those who helped to govern the province.