Richard's son Jonathan was in London in 1773 and Richard Clarke & Sons were named as factors for the Honourable East India Company and were among the consignees of the tea which was thrown into Boston Harbor in December of that year, in the Boston Tea Party. On November 2, they had received a letter signed "O. C.," ordering them to appear at the Liberty Tree the following Wednesday at noon to make a public resignation of their commission as factors. On Wednesday morning some of the other consignees, including Thomas Hutchinson Jr. (son of the governor), Benjamin Faneuil, and Joshua Winslow, met the Clarkes at their warehouse on King Street.

A mob of about five hundred had gathered at the Liberty Tree and, as the merchants did not appear, a considerable number gathered in front of the warehouse. Nine of them went in as emissaries to induce the merchants to yield, and, when they refused to do so, the mob attempted to storm the building but was repulsed. When Jonathan arrived from England there was a gathering of friends at the Clarkes' house in School Street to welcome him, which led to another attack by the mob.

In view of the growing difficulties in Boston, Clarke decided to go to England also, and after a remarkable voyage of only twenty-one days landed there on December 24, 1775, and lived at Copley's house until his death in 1795, at the age of 83.