The Parish Church of St Thomas the Apostle is at least the third, and possibly the fourth building on this site, as there was some tradition of a chapel standing there as long ago as 1483. There is no record of the origin of Ashton Chapel, which is first mentioned in 1515 when there arose a dispute between Sir Thomas Gerard of Bryn and his namesake at Ince. It was then that "Priest at Ashton Chapel" had given notice that Sir Thomas intended to make a straight ditch through Turnshea Moss so that his turf rooms might be drier. Little is known of it for a century after this, but it is recorded that Humphrey Winstanley and Alice Worsley were married in 1559 "in a chapel in the house of Sir Thomas Gerard" by Oswald Key, "Chaplain singing at Ashton Chapel". Oswald Key appeared at the first visitation of Queen Elizabeth's reign.

When Saxton produced his map of Lancashire in 1557, Ashton Chapel was sufficiently important to be included. This first chapel was probably a small oneand may not even have been consecrated "excepting by holding devine service therein", as it was only a chapel of ease to Winwick. As there is no evidence, we can only imagine the interior from what we know of Churches at that time. It was most likely very plain with white washed walls on which Bible stories could have been painted, the floor plain earth or flags, and everyone standing for the services, pews only being introduced on a general scale after the appearance of the reformed prayer book. The congregation probably did not join in the services very much as they would have been in Latin. The Priest's vestments would have been much the same as today, and the altar most likely a plain stone slab on which there would have been a crucifix and candles.
At that time England was still a catholic country, but when Edward V1 became king in 1547 there were great changes, and these must have been felt in the little chapel at Ashton. When Edward died and Mary became Queen in 1553, Catholicism was restored, but five years later Elizabeth re-instated the Protestant religion. In 1562 it was noted that Sir Thomas Gerard forcibly carried to the chapel an old relative, as a too obstinate adherent of the old religion, so the new services of the Elizabethan Prayer Book was obviously used there. Half a century later, at the end of Elizabeth's reign, the Protestant religion was firmly established, but church matters could hardly have been satisfactory in Ashton as the ministrations at the chapel were irregular. In 1590 there was "no preacher there", and more than twenty years later "seldom a curate". The most probable reason for this was that as it was only a chapel of ease to Winwick, there was no income except what the Rector allowed. Only from 1645, when the Minister was granted the sequestered tithes of the township, which were worth £20 a year, do we find a continuous list of curates.

Then came the Civil War when the Bishops and clergy were turned out of their Churches and Chapels. Ashton suffered as all other parishes in the area. In the parliamentarian period, after the Civil War, Lancashire was divided up into nine Presbyterian "Classes". The fourth "Classis" consisted of Warrington, Winwick, Leigh, Wigan and Prescot Parishes. A list of Ministers and Elders fit to be out of this Classis" includes the following from Winwick Parish.

Ministers

Mr Charles Herle of Winwick
Mr Thomas Norman of Newton
Mr James Woods of Ashton

Others fit to be Fourth Classis include

Mr Robert Watmough of Winwick
Gilbert Eden of Winwick
John Ashton of Newton
James Pilkington of Ashton

Every living was closely scrutinised by the Parliamentary Commissioners. Every witness who could give evidence was examined, every particular enquired into, and a voluminous report sent to Parliament. Particulars of these Parliamentary Inquisitions of 1649 and 1650 are to be seen in the Lambeth Manuscripts. The Commissioners in their report represented that:-

"...............there is a chappel situated in Ashton, Fower myles 132 poles and 2 yards from the Parish Church of Winwick, and two myles from Newton chappel, and Mr. James Woodes is Minister there, a very Godly preacher, a man of very good life and conversacon, but did not keep the last fast day appoynted by Acte of Pliamt, for hee had noe orders, And hath for his sallury the Tythe of Ashton, by order from the comittee of plundered Ministers, and came in by free Ellecon of the whole Towne, which said Tythe is worth one hundred pounds and two shillings, and there is also a donatie of Nine Shillings and sixpence p. ann, paied by John Homfryson to the said Mr. Woodes. And in regard to the distinct (distance) from the Parish Church and other Chappells, we psent that it is fitt to bee made a parish, And the rest of Haydock (Excepting those howses presented to bee annexed to Newton and St Ellens) to be ioyned unto the said Parish of Ashton."

The recommendation that Ashton be made a Parish was carried out.

The dissolution of the Commonwealth was soon followed by the fall of the Presbyterian Establishment in Lancashire, which fell almost as rapidly as it had risen. In the interval between the Restoration of the Monarchy and the passing of the Act of Uniformity, the government of the Church was very unsettled, and its services were very far from uniform. The Liturgy was restored by Royal authority, but the Presbyterians had the Kings promise of toleration in the exercise of their ministry.

The Act of Uniformity of 1662 required that "every parson, vicar or other minister whatsoever" should, before the Feast of St. Bartholomew, "openly and publicly before the congregation assembled for religious worship, declare his unfeigned assent and consent to all and everything contained in, and prescribed by, the Book of Common Prayer." It further enacted that "no person should be capable of any benefice, or presume to consecrate or administer the Holy Sacrament, before he ordained a Priest by Episcopal ordination". All ministers who did not comply with the requirements of the Act were deprived of their livings, and if they officiated in any Church, they were subject to fines and imprisonment.

In the Wigan area in 1662, all Nonconformist clergy were ejected from their Chapels. The Rev. James Woods was ejected from Ashton, but he continued to preach for about twelve months, taking services in a farm house, before leaving to live in Cheshire. An entry in the diary of Roger Lowe for April 1663 reads: "Mr. Woods came to take leave of every inhabitant and called upon me. I went with him and with great lamentation at his going, with advice to every family to live well."

Mr. Woods on leaving Ashton went to live at Thelwall, where he died in 1666. Even after his departure it appears that he still had had his followers in Ashton. Another entry in Roger Lowe’s diary for 5th February 1668 tells how he disagrees with "Standing at Gospels," and regards "other ceremonies now in use at Ashton Chapel as mere Romish fopperies."

On the state of things between then and the rebuilding of the chapel in 1714, there is no account, apart from the fact that in 1698 certain prominent inhabitants of Ashton petitioned the Rector of Winwick for a font to be placed in the chapel "for the public Baptism of infants." The signatories to this petition were:

Aurther Launder, Roger Rosbotham, Peter Cook, John Hey, John Birchall, Neamiah Joanes, William Newton, John Wallis, Ralph Johnson, Peter Lowe, William Sixsmith, James Winstanley Edward Marsh, John Knowles, James Johnson, Thomas Potter, John Lowe, Edmond Winstanley, Joseph Birchall, Thomas Lowe, Thomas Lowe, Thomas Johnson, John Darbishaire, William Marsh, Edward Houghton, Mathew Lowe Edward Callon, James Chaddock, James Darbishaire, John Pendlebery, Thomas Gerard, John Birchall, John Lowe, William Hasleden, Bryon Lowe, Thomas Marsh, Raph Lowe, James Orrell, John Ashton, John Callon, James Naylor, William Johnson, James Lowe, John Layland, John Clark, Robert Naylor, Richard Hatton, William Arrowsmith, Nicholas Leech, William Whittel, Jeffrey Birchall, John Naylor, Thomas Richardson, Thomas Hasleden, James Cash.

The petitioners promised to put the chapel into good repair if their request was granted. Although there is no actual evidence, we can picture the interior of this first chapel during the many changes from the reformation in the first half of the sixteenth century until 1714 when it was rebuilt. After the reformation, the stone altar would have been replaced by a wooden table which would most likely have been brought to the centre of the Chancel and positioned length -wise east to west. In 1630 the Chancel would have been changed again when Archbishop Laud caused all the altar tables to be placed against the east wall where the medieval stone altar would have stood. The table might still have been brought forward for the Communion Service. During the Commonwealth, Cromwell changed things yet again, and the table would have been secondary to the pulpit. A small "Holy Table" would have been well forward in the Chancel with very likely a high pulpit directly behind it. In 1662 the position generally reverted to that under Laud, although it became less customary to move the Table. Some years after this, probably towards the end of the century, the Sanctuary would have appeared, divided from the rest of the Chancel by a communion rail. In the list of Curates displayed in the present Church, we have for this early period:-

1570 Oswald Key
1609 John Jannion
1645 James Woods
1663 = Madock
1668 = Atkinson
1690 Thomas Wareing
1710 John Smith

Oswald Key was officiating at Ashton Chapel at the beginning of Elizabeth's reign (1558-1603). It is recorded that he performed a marriage in 1559 in a chapel in the house of Sir Thomas Gerard, which indicates that the public chapel was separate from the private chapel of the Gerard’s.
James Woods was a Presbyterian, who was elected "by the whole town for his scholarship and holiness of life" He was in charge at Ashton as early as August 1645. From the Winwick Registers it seems that Thomas Potter, afterwards of Culcheth was assisting in 1656. Obviously Woods was a man of good life and a good preacher, but he would not give his assent to the new Prayer Book of 1662 and was ejected from the living.

Thomas Wareing was a graduate of Christ Church Oxford taking his BA in 1685. Ashton was probably his first Curacy as he is recorded as performing several marriages at Winwick between 1686 and 1696. In 1707 he became vicar of Garstang where he died in 1772.

John Smith was known to have been in the Parish between the years 1710 and 1731. It was during this period in 1714 that the new Chapel was rebuilt.