On the 13th of November, 1660, Lord Windsor, Lord-Lieutenant of the county, wrote to the Secretary of State--"There is a quaker in prison for speaking treason against his Majesty, and a countryman also, and Captain Yarrington for refusing to obey my authority." [6] It would appear from subsequent letters that Yarranton must have lain in prison for nearly two years, charged with conspiring against the king's authority, the only evidence against him consisting of some anonymous letter's.
At the end of May, 1662, he succeeded in making his escape from the custody of the Provost Marshal.

The High Sheriff scoured the country after him at the head of a party of horse, and then he communicated to the Secretary of State, Sir Edward Nicholas, that the suspected conspirator could not be found, and was supposed to have made his way to London.

Before the end of a month Yarranton was again in custody, as appears from the communication of certain justices of Surrey to Sir Edward Nicholas.[7] As no further notice of Yarranton occurs in the State Papers, and as we shortly after find him publicly occupied in carrying out his plans for improving the navigation of the western rivers, it is probable that his innocence of any plot was established after a legal investigation.

A few years later he published in London a 4to.

tract entitled 'A Full Discovery of the First Presbyterian Sham Plot,' which most probably contained a vindication of his conduct.[8] Yarranton was no sooner at liberty than we find him again occupied with his plans of improved inland navigation.