[5] Over the next six years, Swarthmoor Hall became a centre of Quaker activity; she served as an unofficial secretary for the new movement, receiving and forwarding letters from roving missionaries, and occasionally passing along admonitions to them from Fox, Richard Hubberthorne, James Nayler, and others.

After her husband's death in 1658, she retained control of Swarthmoor Hall, which remained a meeting place and haven from persecution, though sometimes, in the 1660s, raided by government forces.

After the Stuart Restoration, she travelled from Lancashire to London to petition King Charles II and his parliament in 1660 and 1662 for freedom of conscience in religious matters.

While the structure and phraseology of these submissions were quite different, the import was similar, arguing that, although Friends wished to see the world changed, they would use persuasion rather than violence towards what they regarded as a "heavenly" (i.e. spiritual) end.

After this, they spent about a year together at Swarthmoor, collaborating on defending the recently created organisational structure of separate women's meetings for discipline against their anti-Fox opponents.

Surviving both husbands by a number of years, she continued to take an active part in the affairs of the Society including the changes in the 1690s following partial legal tolerance of Quakers, when she was well into her eighties.

In the last decade of her life, she firmly opposed the effort of her fellow believers in Lancashire to maintain certain traditional Quaker standards of conduct (for example, in matters of dress).

[8] Margaret Fell's meeting with George Fox and her subsequent conversion are the subject of the first part of the novel The Peaceable Kingdom by Jan de Hartog.

Some of her more substantial works—including A Call to the Universall Seed of God (1665), Womens Speaking Justified (1666; second edition, 1667), and A Touch-Stone: or, A Perfect Tryal by the Scriptures (1667)—were written during the period of her imprisonment in Lancaster Castle (1664–68).