Often called "Little John" because of his diminutive stature, Nicholas Owen has frequently been called John Owen in error. Owen was the son of an Oxfordshire carpenter, and was himself a skilled builder and joiner prior to entering the Society of Jesus as a coadjutor around 1577. Henry More refers to him as one of the first English lay-brothers.

He returned to England with John Gerard in 1588, landing on the Norfolk coast. It is thought that at around this time he began his job of building hiding places for the Jesuit priests. The earliest examples of his work can be found at Oxburgh in East Anglia, Braddocks and Sawston. There are over a hundred examples of his work throughout central England, although he concentrated on a few specific areas. His work, and the cleverness with which it was executed, saved many a priest from the gallows. His work was most prominent at Hindlip, where he built no less than eleven secret hiding places for its owner Thomas Habington, including the one that Owen himself used in the few days leading up to his capture.

Owen was captured on more than one occasion, although he avoided giving the authorities any clue as to his true identity and thus was released. In 1594 he was transferred from the Marshalsea to the Tower, from which he escaped. He is said to have orchestrated the escape of Gerard from the Tower in 1597. He managed to evade the authorities for another nine years until the discovery of the Gunpowder Plot. He was with Father Henry Garnet, Father Edward Oldcorne, and Chambers at Hindlip when Sir Henry Bromley arrived on 20 January 1606 with orders to search the house for priests and others involved in the Plot. Owen hid with Chambers at this time, and Garnet with Oldcorne.

On the morning of 23 January 1606, due to lack of food, Owen and Ralph Ashley (Chambers) emerged from their hiding place. In time, Garnet and Oldcorne were also captured. Little John was interrogated for the first time on 26 February, at which time he told the authorities nothing, denying his knowledge of Garnet, Oldcorne, and even remained vague about his own aliases. By the time of his second confession, long and painful sessions in the manacles had severely deteriorated his physical condition, and he admitted to attending Garnet at Hindlip and White Webbs, but never gave a single detail on any of the hiding places he had spent his life building. His physical condition at this second interrogation may be judged by the fact that "that his stomach had to be bound together with an iron plate".

He was threatened with further torture, but died soon after on 2 March, 1606 before this could take place. One report on his death stated "they tortured him with such inhuman ferocity that his stomach burst open and his intestines gushed out".

The Government published the story that Owen had taken his own life, but this was clearly untrue: the ordeal had simply been too much for Owen's frail body to withstand. It has also been suggested that the infirmities he suffered during the latter parts of the sixteenth century were as a result of incarceration. Both Garnet and Gerard wrote poignant eulogies on Owen's interesting life and agreed that without his skill, many of them would not have survived as long as they did. In 1970, the Catholic Church recognised Nicholas Owen as a martyr, and he was canonised.

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