Much of the medieval interior was destroyed during the restoration of 1863, though the nave arcades, with their curious unfinished carvings, have survived. It would appear that the nave was enlarged during the second half of the 12thc, by the insertion of N and S aisles, though not as part of the same continuous programme of work. The W tower is also part of the original Norman building, though some sections of the lower stages may have been part of the earlier Anglo-Saxon structure. From internal details, parts of the lower stages of the tower would appear to have been constructed roughly contemporaneously with the three bay N aisle, i.e. early in the second half of the 12thc. The construction of the S aisle, of just two wider bays, would have followed, probably after c. 1170.

It is known that a religious building, in the form of a minster, was in existence on this site as early as the 8thc, through correspondence in 757 between Pope Paul I and Eadberht, King of Northumberland, concerning the appointment of an abbot. The church has also preserved several 10thc carvings of considerable quality, indicating its continuing importance. Before the Conquest, Ulf gave 6 bovates in Stonegrave to the Archbishop of York. Domesday Book records that Ralph Paynel, who held 5 carucates and 2 bovates in Stonegate in 1086, tried to claim the 6 bovates held by the Archbishop, but the church's claim was upheld.

The carvings in the capitals of both N and S aisles are not stylistically consistent and seem somewhat discontinuous. The S aisle is more ambitious than the N in terms of its construction, with its two bays creating a more spacious sense on that side of the church. Also, the waterleaf in the capitals in the S arcade is more finely and competently cut than that seen in the W respond in the N arcade and is more consistent with other examples of this type of carving appearing after c. 1160.

There has been some discussion of the medallion appearing on the S face of the pier capital in the N arcade, in relation to the debate about whether capitals were carved in a workshop and then brought to the site, or if they were carved in situ. The upside down position of the mermaid holding a fish has been interpreted as evidence of the block having been carved off site, with the mistake not having been realised until it was set on top of the pier (Zarnecki (1951), 73-91). However, if the suggested sequence of carving was followed (ibid. 79), is it likely that the sculptor would not have realised that the figure would be upside down? The carving of the adjacent medallions are both intricate in conception and crisp in execution, and are surely the work of a relatively accomplished craftsman who would have been unlikely to have made such an error. Also, in this instance, the mermaid appears to be holding a fish and not a mirror, consistent with the more traditional symbol of vanity. Not too far away, there is an example of a very early Romanesque carving of a mermaid in the Norman Chapel at Durham Castle. There could be a more localised explanation for this unusual subject. There is evidence from the 13thc of royal rights being granted for the staging of weekly markets and a large annual fair at Stonegrave, which may indicate its importance as a centre for trade and commerce. This could be a reference to local trade, with more planned to appear in the uncarved medallions.

The unfinished condition of several other faces of this and other blocks suggests that the work was interrupted by the loss or departure of the master mason, whilst the work was still in progress. The other potential explanation could be the emerging influence from the newly established Cistercian Abbey at nearby Rievaulx. Their distaste for ornament may have had some impact on what was clearly the abandonment of a more extensive series of decorative motifs.

It would seem likely therefore that the carvings in the north arcade date from a period c. 1150-1160, with those of the south arcade appearing around 1170.