Throughout his life he worked for the abolition of slavery. During the politically turbulent 1790s, Pye-Smith took over the editorship of the Sheffield Iris, the leading abolitionist newspaper in the North of England, during the imprisonment of its editor, his friend James Montgomery. In 1830 Pye-Smith took the Chair of the Board of Congregational Ministers when it passed an anti-slavery motion to secure support from all Congregational chapels across the country in petitioning parliament: "That we feel it to be a solemn duty to employ our influence with our congregations and the public, to promote petitions to both Houses of Parliament for the abolition of Colonial Slavery, and therefore pledge ourselves, and beg to recommend to our brethren throughout the kingdom to prepare from each congregation such petitions to parliament..." The Congregationalists' 1833 abolition lecture, "The Sinfulness of Colonial Slavery", was delivered at John Pye-Smith's Meeting House in Hackney by his former pupil, Robert Halley.
