The interior effect of St Dogfan's is dominated by its unusual layout and the uniformity of its roof heights, perhaps partly due to the C19 restorations, although already remarked as a 'singular arrangement' by Glynne in 1850. The entrance at the north side by the C19 porch opens into a transverse passage at the foot of the chancel steps, uniting the north and south aisles and the nave. The aisles extend eastwards and only overlap one bay of the nave. The main space available for a congregation, in the north aisle, is oddly at the rear of choirstalls. Borrow in 1854 described the interior as sombre 'from the heaviness of the architecture'.
The nave is paved with red and black quarry tiles; the walls are plain, without monuments, and the ceiling is a plain barrel vault (thought to conceal mediaeval timbering). At west the nave abuts the tower, with a traceried Gothic style screen incorporating double doors with side-lights and a leaded clerestory giving borrowed light to the ringers' floor of the tower. At east the nave has a slight arch (described in the Inventory as 'a plain oak rib') at the line where the aisles commence. C19 open pews of plain design in pine.
In the eastern part of the church the chancel is raised two steps above the nave and aisles floor level, and there is a C19 restored arcade of three arches each side. Plain pine choirstalls, pulpit and prayer desk. Because of the unusual layout the pulpit and prayer desk are to the east of the choirstalls. Patterned floor tiling in quarry tiles with encaustic features. The plain barrel ceiling of the nave continues over the chancel, but the last bay, over the sanctuary, is a late mediaeval barrel shaped celure with carved crowsfoot bosses to the rib intersections and a carved cornice. The sanctuary is one further step up and there is a brass Communion rail and a richer patterned floor with encaustic features. Above and to the sides of the altar are a carved Gothic reredos and side panelling, the reredos incorporating a carving of Leonardo's Last Supper in high relief. The altar table (1794) now stands in front of the altar step, a little forward of the reredos.
The north aisle is of five bays with collar-beam trusses. Black and red quarry tile paving. Plain pews facing south. Octagonal font close to the door, inscribed IA / 1665 / RI / V / HT, recording the initials of the vicar and churchwardens, on an earlier octagonal base.
The south aisle is mainly occupied by the organ. Barrel ceiling; black and red quarry tile paving. Plain pews facing north. Thirteen wall memorials have been collected on the west wall against the vestry. At centre is a large memorial to the Rev. William Roberts of Whittington and Selattyn, slate ground, marble urn above an oval plaque . Other memorials of the C18 and later, including to Dr William Worthington, vicar . Brasses of 1740 and 1792. Another C18 stone behind the organ. An early Celtic stone (the Cwgan stone) was recovered from the stonework of the south aisle during the restoration of 1882 and now stands against a pier of the arcade: this is a Celtic cross in shallow relief with contrasting surface patterning each side.
Single light stained glass window at south depicting the Good Shepherd by Curtis, Ward and Hughes, commemorating Canon Jones, vicar, and his daughters . C20 east window in north aisle depicting St Asaph and St Dogfan.