During the archaeological survey of the Auld Kirk and Anchor Green in 1999 a burnt circle and Roman coins were discovered suggesting there was a Christian settlement there in the 7th century. The island where the Auld Kirk is sited was thought to have been used by Saint Baldred as a sanctuary in the 8th century. The church was substantially enlarged in the 13th century when a bell-tower was added. The ruined walls exposed by Dr. James Richardson during the 1951 excavation give an indication of the outline of the Auld Kirk, although a considerable section on the east fell into the sea following a great storm in 1656. The bell was transferred to the church in Kirk Ports in 1664 and is presently on display outside the St Andrew Blackadder Church. The only surviving building on the Anchor Green is the entrance porch of the Auld Kirk which was converted into a bothy in the 1850s when a fireplace was installed on the north wall.

The Parish Church in Kirk Ports surrounded by elm trees was erected in 1664 and renewed in 1770; and except for the old oak seat of the Dalrymple family, in the front of the gallery, the interior was wholly renewed in 1819. The church contained an hour sand-glass to regulate the service, a metal baptismal ewer, an iron alms-box to secure the offerings and four silver chalices which were believed to have descended from the Episcopalian period and then passed into the service of the Presbyterian Kirk. One is dated 1670 but at least two of the cups are from an earlier age. There was accommodation for 550 people with seats in the gallery allocated to the proprietors and tenants, and half of the western gallery allotted to the magistrates, council and burgesses of the town. In the 1860s a parapet wall was erected with iron railings along the north and west sides, with the manse built in 1825 to the south west, on an elevated position at the Glebe.

During the middle ages the Church administered law and order. The majority of cases before the elders of the kirk session were concerned with sex, sometimes known as the 'Bawdy Court'. The most common prosecutions were for heresy, divorce, deformation, adultery and fornication. If found guilty the offender was ordained to make public atonement before the congregation the following Sunday and pilloried on the stool of penitence. A metal neck collar known as a 'Joug', attached to the wall of the old Parish Church in Kirk Ports and used to hold offenders is on display in the local museum.

The Church did not have the power to inflict physical punishment, but if the offender refused to repent, they were excommunicated from the Church and sent to damnation. In more serious cases the offender was handed over to the secular powers of the State for the Privy Council to decide their fate. The Church of Scotland also administered the registration of births, marriages and burials from 1538, this record did not include Roman Catholics and other religions. During the 18th century if a person was accused of being a thief they would sue in a 'secular court' or Sheriff Court while moral offences continued to be heard in the 'spiritual court'.

By 1830, a large part of the Church's legal authority had been taken over by the State except the settlement of disputes over wills which continued until 1855. The court records from the old Parish Church in Kirkports survive to this day and the colourful entries document the morals of this small town through the ages.

In the graveyard is a headstone erected by public subscription in memory of Johnnie Bowers, the last of the North Berwick town criers, who died in 1878. The stone bears a portrait carved by local mason Walter Skirving which was generally recognised as a faithful likeness of the old worthy. It was said that Bowers scorned the conventional hand-bell using instead two earthenware bowls which he rattled together as a preliminary to his public announcement. The graveyard is also the burying place of many native families including the Dalrymples, Yules, Crawfords, Buchans, Walkers, Burns, Begbies, Robertsons, Grieves, Edingtons, Whitecrosses and Brodies.

There was a Christian meeting-house in Westgate erected by the United Associate Synod in 1778 and rebuilt in 1832. The minister was paid from the collection and seat rents. This group known as the 'Dissenters' had 232 members and their building was situated on the ground now occupied by Nos. 45-51 Westgate.

On 18th May 1843, 190 clergymen walked out of the General Assembly of the Church of Scotland over the vexed issue of patronage, whereby local lairds could appoint the minister of a parish. A few days later some 500 ministers met at Tanfield in Edinburgh to sign the Deed of Demission and established the Free Kirk.

A year later, the Blackadder Free Church was constructed in Shore Street (named after the covenantor John Blackadder) with Rev. John Shewan as minister. The United Presbyterian Church ( Abbey Church) designed by Robert R. Raeburn was erected on the site, formerly an eyesore of the 'Burnt Houses' in 1868 with the Church Hall added in 1890 on land used by the Bowling Club.

A group known as 'All Saints' held their meetings in the Schoolhouse at the corner of Church Road and High Street before the Scottish Episcopalian Church was built in 1861, designed by John Henderson. After its erection it was found too small to contain the congregation in summer and was considerably enlarged. It was consecrated in 1863 by Samuel Wilberforce then Bishop of Oxford and named St Baldred. Sir Hew Dalrymple gave a free site for it and Lady Mary Nisbet Hamilton contributed largely to the costs of the construction. The porch and ornamental carved entrance doors were designed by Sir Robert Lorimer in 1901. Following the Restoration of the Catholic hierarchy in Scotland in 1878, the Roman Catholic Church (Law Brae) was erected by Dunn and Hansom in 1879, where the 'League of the Cross' instituted by Father Mackenzie also held their meetings. The chancel was built by Basil Chanpreys in 1889 and the Lady Chapel designed by Sir Robert Lorimer was added in 1916. The Parish Church of St Andrew (High Street) designed by Sir Rowland Anderson was built in 1883 with the tower added in 1907 when the clock was presented by the Town Council. The Kirk Session chair is believed to have been one of the ancient oaken chairs brought from Tantallon Castle on its final demolition.

The old Parish Church bell now on display outside the church in St Andrew Street dates back to the Auld Kirk at the harbour and is inscribed round the top - 'Jacobus Monteith me fecit, Edinboch, pro Templo de Northberick. Anno Domini, 1642. Spero Meliora', which translates as - 'James Monteith made me at Edinburgh, for the Church of North Berwick, in the year of our Lord 1642 - I hope for better things'. After twenty-two years of service at the Auld Kirk Green, it was moved in 1664 to the new church in Kirk Ports. There it rang people to worship for two hundred and nineteen years until 1883 when the congregation moved to the new building in the High Street. It continued to ring in the old tower for another twenty-four years until 28th July 1907 when the clock tower was completed and the bell transferred. In 1928 a new bell was gifted by John Menzies,(5 West Bay Road), founder of the bookstall and newsagent company.

The Evangelical Meetings were held in the Fisherman's Hall with Mr. J. Scroggie conducting the service. It was not uncommon for visiting dignitaries, enjoying a holiday in North Berwick, to be asked to perform various duties. In 1892 the Lord Mayor of London opened the Blackadder Church Bazaar and in 1902 the Prime Minister, A.J. Balfour opened a Sale of Work in the Foresters' Hall.