In 1683, he was forced into exile in the Dutch Republic due to his involvement in the 1683 Rye House Plot, an alleged attempt to assassinate Charles II and his Catholic brother James.

At the opening of Parliament in October 1673, during the Third Anglo-Dutch War, Ayloffe threw a sabot under the Speaker's chair, supposedly a reference to French influence on the country.

[10] As part of du Moulin's group, he helped smuggle propaganda into England, including pamphlets attacking Stuart foreign policy, their government and monarchy in general.

During this, the sabot incident was used as evidence he was "mad", though Tory politician and lawyer Sir Thomas Meres argued "Mr. Ayliffe is a man of good sense, and points at what he intends".

[15] The most prominent opposition leaders in Holland were Archibald Campbell, 9th Earl of Argyll, convicted of treason in 1681, and Charles' illegitimate son, James Scott, Duke of Monmouth, exiled for his involvement in the Rye House Plot.

[16] Unfortunately, Argyll's Rising failed to attract significant support, and was fatally compromised by divisions among the rebel leadership, Ayloffe and Rumbold being among the few to emerge with any credit.

In his entry for 30 October, diarist Roger Morrice wrote "Mr. John Ayloffe died this day about 11 a Clock over-against the Temple, he was very composed and sedate".

[17] The official account of his execution, penned by L'Estrange, which depicts a repentant Ayloffe offering prayers for the King, the people and the Protestant religion, appears so completely inconsistent with all of his recorded opinions and behaviour it is likely propaganda.

In addition, his biographer George de Forest Lord attributed to him a number of verse satires previously assigned to Marvell, based on several distinct characteristics of Ayloffe's writing.

These include a bitterly anti-French, anti-Irish, and anti-Catholic tone; comparing the Stuarts with Roman tyrants, who threaten the rights of Magna Carta; a "sombre and humourless" quality; and visionary imagery.