Sir Ascelin de Waterville is credited with rebuilding the church as a thank offering for his safe return from the third Crusade (1189-92). Of this date there is only the stiff-leaf decoration on the respond supporting the east end of the north transept arch. The south transept arch may also be of the same date although the east window tracery, a replacement of 1862, in this transept is in the style of c.1300, the same date as the east and north buttresses supporting the chancel. The west tower was rebuilt in the late C13 and the entire church was extensively restored in 1861-3 by William Slater, who was responsible for many other church restorations in Northamptonshire, and all traces of the old furnishings and decoration were swept away. The chancel arch, north aisle, arcade, the tower arch, porch, the oak roof, and interior furnishings nearly all date from this restoration. In this respect the interior is a good example of the influence of the Oxford Movement, which began between 1833 and 1845, rejecting the Protestant element in Anglicanism in favour of the pre-Reformation Catholic tradition. Although St John's was not noticeably High Church the altar, as in most churches in the C19, became the focus of the service rather than as previously, the pulpit. Here at St John's the altar is approached by a chancel raised by one step and the sanctuary by two more steps, with the altar finally set one step above the sanctuary. The then enormous sum of £2,300 was raised by voluntary subscription to pay for the restoration, although Lord Lilford's family, descended from Sir Thomas Powys, contributed the greater part.
In 1778 the old church at Lilford was demolished, part was erected in Lynches Wood to the SW of St John's and some of the monuments moved to Thorpe Achurch. The oldest is to Arthur Elmes (d.1663), a tablet in the tower (the Elmes lived at Lilford Hall), the large monument in the north transept is to Sir Thomas Powys (d.1720) who bought Lilford Hall from the Elmes in 1711. This 20ft high monument is signed by Robert Hartshorne and is his acknowledged masterpiece, Sir Thomas, a judge of the Queen's Bench and premier Serjeant at Law, reclines in his judge's robes flanked by the figures of truth and justice. Later Powys monuments are those to Charles (d.1804), and Henry who died at the siege of Badajos in 1812 leading the final assault, and Henrietta Maria (d.1820).
The oldest g1ass, in a small window in the west end of the tower, is by Clayton & Bell dating from 1863. The east window, a good piece of glass, is attributed to Cox & Buckley and dated as being after 1880. In the south chancel, the east window, by an anonymous maker is a skilled piece of work influenced by the Arts and Crafts movement and commemorating the 4th Lord Lilford (d.1896). The large iron-bound wood chest beneath the north transept arch may date from the mid-C 16 when it became mandatory, from 1538, to keep registers of christenings, marriages and burials. It was used to lock up church silver and the registers. The Litany Desk was a congregational gift in memory of the rector, Herbert C Holmes (d.1902). Four bells in the west tower are dated: (1) 1861, (4) 1735 and (2) and (3) were recast in 1898. In 1912 the organ and organ chamber were panelled in oak and the sanctum floored with marble.
A noteworthy, and colourful, rector of Thorpe Achurch from 1592 until his imprisonment in 1630 was Robert Browne, a Puritan separatist and founder of the Brownist Movement, a forerunner' of the Congregationalists, Brown took orders but his licence to preach was withdrawn when he attacked the established church. In c.1580 he formed a congregational society in Norwich maintaining that the connection between church and state had no foundation in scripture and that the congregation and pastor derived their authority only from God. Browne with his congregation were forced to take refuge in Middleburg in Holland. He returned to England in 1584, was reconciled with the established church and reordained in 1591, taking up his duties in Thorpe Achurch the following year. Browne, always a man of violent temper, was gaoled in 1630 for assaulting a constable, where he died three years later.
Outside the church note two scratch dials on a south transept buttress. As the church has no clock the verger would use these to judge when to ring the bells for services. The west door of c 1300 is original but badly weathered and the attractive lych-gate, designed by his widow, commemorates the 4th Lord Lilford who died in 1896.