John Payne was a native of the Diocese of Peterborough, but the date of his birth remains unknown. There has been some speculation about his early life, but his first association with Essex seems to have been as a steward to the Shelley family of Stondon Hall. He was ordained at Cambrai on April 7th 1576 and left for England shortly afterwards with St. Cuthbert Mayne.

He acted as chaplain and steward to Lady Petre at Ingatestone Hall and also ministered to Catholics in the district. He worked further afield too and is known to have taken lodgings in London. A successful pastor, he was brought to the attention of the authorities and was imprisoned during the winter of 1576-77.

On July 2nd 1581, John Payne celebrated Mass at the house of William Moore at Haddon, Oxfordshire. Amongst the worshippers was George Elliott, the notorious informer. A few days later, Payne was arrested in Warwickshire. On July 4th, he was examined by Lord Walsingham at Greenwich and was committed to the Tower of London. He was subsequently charged under the Statute of Treasons (1352) for having plotted against the life of the Queen. Elliott claimed that Payne had tried to enlist his support. Payne was tortured twice whilst in the Tower, but refused to admit the accusations made against him.