All that survives of the old church at Peterhead is the chancel arch, part of the chancel and a west tower with the west wall of the nave attached. Of these, only the chancel arch and associated chancel walls appear to be of medieval date and are arguably Romanesque. The nave, itself, no longer exists, but it appears to have been long and narrow, with "an aisle on the north side" (Scottish Notes and Queries. 1889), which may mean either an aisle along the north side of the nave, in the usual sense, or an extension built outwards from the north side, as is common in post-Reformation churches in Scotland, where such additions are also called aisles. A town plan of 1739, by John Jaffray and R. Cooper, has a rough drawing of the church next to the 'Kirk-burn', which shows the south side of the church, with its west tower, nave and lower chancel intact. The centre of the parish of medieval Peterhead was at Peterugie/Inverugie Petri and the first post-Reformation minister of the church was Gilbert Chisholm, last prior of Deer Abbey, who held charge of Peterugie, Deer, Foveran, and Longley until 1569. In 1560, Queen Mary of Scotland had appointed Robert Keith as Commedator of Deer and in 1587, King James VI of Scotland raised this same Robert to a peerage, with the Deer Abbey lands as his temporal lordship. In 1593, there were just 14 feus in the parish, but with the development of the harbour, the town grew quickly. The parish was split into two about 1620, a second church being built in Longside (about 7 miles west of Peterhead town centre). In 1637, William Keith, Earl Marischal, obtained a new charter of the Deer Abbey lands, which included the tithes of the parish of Peterhead and the parsonage of the church there. George Moir was the last minister to serve the Old Church, before moving into a new church on a different site in 1770. Within thirty years this second church had become ruinous and was taken down. It's successor, built in 1804-6, survives.

Old Deer was an ancient church, founded by St Drostan in the 6th century. In 1218, Deer Abbey was founded nearby, at which time Old Deer was given to it, along with Peterugie (Peterhead). It is uncertain when Old Deer, itself, first gained control of Peterugie, but it has been suggested that it was either in the 12th century (possibly 1130s) or about 1218. At the Reformation, Peterugie was listed as being under the control of the abbey. A 1275 taxation for the deaconry of Buchan in the diocese of Aberdeen lists 'Innerugy Petri' for both its rectory and its vicarage (Registrum Episcopatus Aberdonensis).

Although a 12th-century date is frequently given for the chancel arch of the Old Church at Peterhead, other dates have also been suggested, including a date in the 13th century, as well as in the 17th century. All seem to accept that the west tower is a post-Reformation structure and a surviving bell of 1642/1647 suggests that it had been completed or was under construction by this date. The impost profile of the chancel arch fits well into a Romanesque context, but the capitals are more enigmatic. Are they idiosyncratic cushion capitals based on types found on, for example, square piers in the east end of Kirkwall Cathedral (Orkney), nave responds of St Barthomew's, Smithfield (London) or on an arch at Whitwell (Derbys.), or are they of a minimalistic later-12th century type (as on the preserved doorway of Lamington, Scotland)? Normally, capitals like this would have some sort of shaft beneath them, but there are 12th-century sites elsewhere that can be paralleled, as can be seen also at Whitwell, Kirkwall and St Bartholomew's Smithfield. It seems highly unlikely that the chancel could have been built post-Reformation, as the new Protestant churches were orientated differently, without eastern chancels, focusing on a central preaching pulpit. The church ruins at Longside, built in the first half of the 17th century when the parish of Peterhead was split into two parts, for example, has the usual rectangular form common for this date. It is difficult to place the imposts of Peterhead's Old Church much beyond the 12th century, but the debate over the capitals is likely to continue.