Pilkington was an early Whig politician of the Exclusion Crisis, and was returned as one of the four City of London members to the short Parliament which met on 6 March 1679.
Meanwhile, the lord mayor, Sir John Moore, who led the court faction in the city, gave similar entertainments to its chiefs at his house in Fleet Street.
Roger North claimed in his Examen that, on the trial of the Earl of Shaftesbury for high treason (24 November 1681), Pilkington showed great partiality in returning the grand jury, and was reprimanded by the judges.
In March 1682 Pilkington himself was tried at the Southwark assizes on a slight charge of libel, when the jury brought in a verdict of £800 damages for the plaintiff.
Pilkington appealed on the ground of excessive damages, and eventually the case came before the House of Lords, by whom the judgment was confirmed 3 June 1689.
Pilkington's shrievalty closed on 28 September 1682, when the outgoing sheriffs declined to entertain, according to custom, the lord mayor at dinner.
The alleged riots fomented by Pilkington and Shute were made in part the ground for suspending the city's charter by the quo warranto of 1683.
On the flight of his old enemy, then King James II, and the arrival of the Prince of Orange in 1688, Pilkington enjoyed the royal favour.
On the sudden death of Sir John Chapman, Lord Mayor, on 20 March 1689, Pilkington was elected for the remainder of the year.