It is Gothic in style, built mostly of tooled granite rubble, and has a cruciform layout with an east–west oriented nave, transepts to the north and south, and a slender tower at the south-west corner.

Its interior is lavishly decorated with polished granite columns topped with ornately carved capitals, marble chancel furniture, and many stained glass windows depicting saints and biblical scenes.

St Margaret's Church is located in a secluded woodland setting, at the end of a long drive leading uphill from Aberlour's High Street.

A chancel, somewhat narrower and shorter than the rest of the building, protrudes from the eastern end of the nave;[4] its east gable has lancet windows, the central one taller than the outer two, all below a single continuous hood mould.

[2] At the west end of the nave is a font, with an elaborately carved wooden cover that originally came from Christ Church in Lancaster Gate, which was demolished in 1977.

[2] The focus of the church is its chancel, at the east end of the building, which is raised up above the level of the nave and separated by an intricate metal rood screen.

[4] The chancel houses an array of original furniture, including sedilia, a reredos and altar, all intricately carved in Caen stone, also by Dawson & Strachan, and a brass tabernacle, designed to appear mediaeval, by J. W. Singer and Sons, who also made the sanctuary lamp.