Following a political crisis in England and the accession of Queen Anne to the throne in 1702, a Tory ministry emerged that sidelined most of Nicholson's Whig patrons. Despite his best efforts to retain his post, he was recalled and replaced in 1705 by Edward Nott. He returned to London, where he was active in the Society for the Propagation of the Gospel in Foreign Parts, and was awarded membership in the Royal Society for his scientific observations of North America. He also acted as a consultant to the Board of Trade, and thus maintained an awareness of colonial issues.