It is highly probable that he did so, for, until the Restoration of 1660, he was regularly in communication with the Royalists, while serving the parliament, or Cromwell, so long as their service was profitable, and making no scruple of applying for grants of the confiscated lands of the king's Irish friends.

[2] In the First Anglo-Dutch War (1652–1654), he served in the navy of the Commonwealth of England, commanding squadrons at the battles of the Kentish Knock (1652), Portland, the Gabbard and Scheveningen (1653).

In 1654, he offered to carry the fleet over to the king, but in October of the same year he had no scruple in accepting the naval command in the expedition to the West Indies sent out by Cromwell.

The crypto-Jewish population following the strengthening of the church aided the English who seized the less desirable island for the Commonwealth régime, and Penn established the Jamaica Station there.

[6] He played a small part in the Restoration:[2] in May 1660 he was on the Earl of Sandwich's ship, the Naseby), which was sent to bring King Charles II home to England from his exile at Amsterdam in the Dutch Republic.

In the Second Anglo-Dutch War, he was flag captain at the Battle of Lowestoft (1665), serving under James, Duke of York, and later in the same year was admiral of one of the fleets sent to intercept Ruyter, despite suffering from gout.

[11] A key source for the adult life of Penn is the diary of his colleague at the Navy Board, and next door neighbour in Seething Lane, Samuel Pepys.

He is also referenced in an entry from 1665, which states, "At night home and up to the leads [roof], were contrary to expectation driven down again with a stinke by Sir W. Pen's shying of a shitten pot in their house of office".

The diary entry for 4 July 1666 includes a long account of Penn's analysis of what was to be learned from the Four Days' Battle, which ended with the statement, "He did talk very rationally to me, insomuch that I took more pleasure this night in hearing him discourse then I ever did in my life in anything that he said."

William Penn had wanted to call the land "New Wales", which was objected to by the Secretary of State, Privy Council member and Welshman Leoline Jenkins.