There has been a house on the site since the 15th century. From 1777 to 1857 it was owned by the Thornton family and in 1784 was known as Mugger-hanger Lodge and described as:

'A neat convenient Dwelling-House, fitted up in a genteel Stile, provided with useful Offices, Coach houses and Stabling, Shrubbery, and Kitchen Garden, on a delightful Eminence, commanding rich Views for a vast Extent.'

During 1790 - 1816 it was rebuilt by Sir John Soane RA (1753-1837), who had built the Bank of England, Dulwich Picture Gallery, and remodelled 10 & 11 Downing Street, and 12 & 13 Lincoln's Inn Fields, which is now the Sir John Soane's Museum.

In 1791 Humphry Repton was working on the grounds at Francis Pym's house, Hassells, in nearby Sandy. The following year he came to Moggerhanger and described the house in his Red Books (1792 and 1798):

'It is too large and too much ornamental for a farm house, while it is too small and too humble for a family country-seat, and its distance from the capital is too great to permit its being called a villa. I shall therefore consider it as an occasional sporting-seat'.

The estate when sold in 1857 comprised 2,056 acres and the house stood in a richly timbered park of 130 acres.

In 1919 having passed through several hands it was acquired by the Bedfordshire County Council as a Sanatorium, first for TB and then as an Orthopaedic Hospital. At this time it was known as Park Hospital. The hospital closed in 1987 and was acquired by Twigden Homes as a building site. They planned to build on the kitchen garden but had no use for the main house, which was a listed Grade II* Georgian building. In June 1997 the house was uplisted to Grade I when it was discovered that it was such an important part of John Soane's work. The grounds were included in May 1997 in English Heritage's Register of Parks and Gardens of Special Historic Interest in England Grade II.

In 1995, the house was legally acquired together with 15 acres for a cost of just £1. The Preservation Trust had to prove that they had the means to do the necessary legal alterations (estimated at just £350,000 in 1993), when they were first offered the house. At the time they had only £50,000 in the bank but urgently wrote to their supporters asking for gifts and interest free loans to be in their bank in ten days' time. By the appointed time, nearly half a million pounds came in!

The various Christian charities on the estate have been in occupation of the stables, the bungalow and gatehouses on the estate since 1994, which they were able to purchase for £155,000. The first phase of restoration work involved the replacement of the roof, which had badly leaked with consequent damage to the internal fabric of the building. At about this time, the trust obtained a £1.2 million grant from the Landfill Tax in order to buy back the walled gardens and woods, which formed part of the original estate, and in 1998, they obtained a £3.3 million grant from the Heritage Lottery Fund to restore the house and grounds.

This grant enabled the next phase of work to begin: the re-rendering of the external walls and this was completed in 2000. The final - and most complicated phase in the House restoration - started in August 2002. This work saw the restoration of the interior of the building, and grew in complexity (and cost!) as it developed, mainly due to the fact thata number of fascinating historical discoveries were made during the restoration work. The house finally re-opened to the public in May 2005.

The first ever Christian martyr in England was St Alban. Moggerhanger is in the diocese of St Alban's, although Moggerhanger Park itself is ecumenical.

The area has many Christian associations. Moggerhanger was in the Parish of Blunham, a neighbouring village, until 1860. One of the incumbents at Blunham being the poet John Donne (1572-1631). There is a Thornton family mausoleum at Blunham church. Bedfordshire is also Bunyan country and John Bunyan (1628-1688) would have called at all the houses in the neighbourhood in his trade as a tinker.

The Thornton family has always had Christian connections. Henry and John, who were cousins of Godfrey and Stephen Thornton at Moggerhanger, were members of the Clapham Sect, and known associates of Wilberforce and later Shaftesbury. All members of the sect were also involved in the Bible Society from its foundation in 1804. In fact the Thornton family have been involved in CMS, the Bible Society, the Church, and banking down through the centuries.

John Newton (1725-1807) and William Cowper (1731-1800) were not far away in nearby Olney. Mrs Dawkins who lived at the house with her husband the Revd Edward Henry Dawkins, built the parish church of Moggerhanger, St John the Evangelist, in 1860 in memory of her husband.