Having invited the Indians to meet him, many chiefs and persons of distinction, appointed to represent them, came to see him. To these he gave several valuable presents, the produce of English manufactures, as a testimony of that treaty of amity and good understanding, which, by his benevolent disposition, he ardently wished to establish with the native inhabitants. He made a most favorable impression upon the savages, and thus secured to Pennsylvania their favor. He then more fully stated the purpose of his coming, to the people, and the benevolent object of his government, giving them assurances of the free enjoyment of liberty of conscience in things spiritual, and of perfect civil freedom in matters temporal. He recommended to them to live in sobriety and peace one with another. After about two years residence in the country, all things being in a thriving and prosperous condition, he returned to England; and James II. coming soon after to the throne, he was taken into favor by that monarch, who, though a bigot in religion, was nevertheless a friend to toleration.

At the revolution, being suspected of disaffection to the government, and looked upon as a Papist or a Jesuit, under the mask of a Quaker, he was examined before the Privy Council, Dec., 1688; but, on giving security, was discharged. In 1690, when the French fleet threatened a descent on England, he was again examined before the council, upon an accusation of corresponding with King James, and was held to bail for some time, but was released in Trinity Term. He was attacked a third time the same year, and deprived of the privilege of appointing a governor for Pennsylvania; till, upon his vindication, he was restored to his right of government. He designed now to go over a second time to Pennsylvania, and published proposals in print for another settlement there; when a fresh accusation appeared against him, backed by one William Fuller, who was afterwards declared by parliament to be a notorious imposter. A warrant was granted for Penn's apprehension, which he narrowly escaped at his return from the funeral of George Fox, the founder and head of the Quakers. He now concealed himself for two or three years, and during this recess, wrote several pieces. At the end of 1693, through the interest of Lord Somers and others, he was allowed to appear before the king and council, when he represented his innocence so effectually that he was acquitted.

In 1699, he again went out to Pennsylvania, accompanied by his family, and was received by the colonists with demonstrations of the most cordial welcome. During his absence, some persons endeavored to undermine the American proprietary governments, under pretence of advancing the prerogative of the crown, and a bill for that purpose was brought into the H. of Lords. Penn's friends, the proprietors and adventurers then in England, immediately represented the hardships of their case to the parliament, soliciting time for his return, to answer for himself, and accordingly pressing him to come over as soon as possible. Seeing it necessary to comply, he summoned an assembly at Philadelphia, to whom, Sept. 15th, 1701, he made a speech, declaring his reasons for leaving them; and the next day he embarked for England, where he arrived about the middle of December. After his return, the bill, which, through the solicitations of his friends, had been postponed the last session of parliament, was wholly laid aside.

In the year 1707, he was unhappily involved in a suit at law with the executors of a person who had been formerly his steward, against whose demands he thought both conscience and justice required his endeavors to defend himself. But his cause, though many thought him aggrieved, was attended with such circumstances, that the court of chancery did not think it proper to relieve him; wherefore he was obliged to dwell in the Old Bailey, within the rules of the Fleet, some part of this and the ensuing year, until such time as the matter in dispute was accommodated.

In the year 1710, the air of London not agreeing with his declining constitution, he took a seat at Rushcomb, in Buckinghamshire. Here he experienced three successive shocks of apoplexy in 1712, the last of which sensibly impaired his memory and his understanding. His religious zeal, however, never abated, and up to 1716, he still frequently went to the meeting at Reading. Two friends calling upon him at this time, although very weak, he expressed himself sensibly, and when they were about to take leave of him, he said, "My love is with you; the Lord preserve you, and remember me in the Everlasting Covenant."

After a life of ceaseless activity and usefulness, Penn closed his earthly career on the 13th of May, 1718, in the seventy-sixth year of his age. He was buried at Jourdans, in Buckinghamshire, where several of his family had been interred.