[3] On 27 April 1570, the papal bull Regnans in Excelsis excommunicated Queen Elizabeth I and those who obeyed her laws and commands, releasing her subjects from their allegiance to her.

Warned by Thomas Ford, Mayne evaded arrest by going to Cornwall and then, in 1573, to the English College, Douai, now in northern France.

On 8 June 1577, the High Sheriff of Cornwall, Richard Grenville, conducted a raid on Tregian's house during which the crown officers "bounced and beat at the door" to Mayne's chamber.

On gaining entry, Grenville discovered a Catholic devotional item, an Agnus Dei, around Mayne's neck, and took him into custody along with his books and papers.

At the opening of the trial on 23 September 1577 there were five counts against him:[4] first, that he had obtained from the Roman See a "faculty" (or bulla), containing absolution of the Queen's subjects; second, that he had published the same at Golden; third, that he had taught the ecclesiastical authority of the pope and denied the queen's ecclesiastical supremacy while in prison; fourth, that he had brought into the kingdom an Agnus Dei (a Lamb of God sealed upon a piece of wax from the Paschal candle blessed by the pope)[5] and delivered it to Francis Tregian; fifth, that he had celebrated Mass.

On the fourth count, he said that the fact he was wearing an Agnus Dei at the time of his arrest did not establish that he had brought it into the kingdom or delivered it to Tregian.

The trial judge, Justice Sir Roger Manwood,[6] directed the jury to return a verdict of guilty, stating that, "where plain proofs were wanting, strong presumptions ought to take place".

[8] Tregian was sentenced to die but was in fact incarcerated for 28 years[9] until, on the petition of his friends, he was released by King James I.

Before being brought to the place of execution, Mayne was offered his life in return for a renunciation of his religion and an acknowledgement of the supremacy of the queen as head of the church.

A. L. Rowse sees the condemnation of Mayne as arising from local rivalries between Protestant coastal and Catholic inland interests.

Establishing a threat from subversive Catholic elements also served Elizabeth's counsellors such as Lord Burghley in their attempts to persuade the Queen to support the Dutch Revolt against Spain.

[15] Christopher M. B. Allison suggests that the silver reliquary discovered in 2015 at Jamestown, Virginia in the grave of Captain Gabriel Archer (died 1609/10) may contain a relic of Mayne.

[20][21][22] Stained-glass windows represent him in the following churches/schools: In the historical novel The Grove of Eagles by Winston Graham, which is set in Cornwall some years after Mayne's death, there are several references to him.

The brother, filled with guilt for his share in the execution, has not only converted to the Roman Catholic faith but is risking his life by sheltering other priests.