In about the year 1500, during the time of the Blessed Margaret of Lorraine, a new master builder, Jehan Lemoine, made substantial changes to the architectural project of the church.

[2] He built the elaborate Porch of the Transfiguration on its west side, and decorated the nave with its current star-patterned vaults and richly-decorated ribs, supported on the outside by two ranks of flying buttresses.

[5] By virtue of its connection with the Martin family and in recognition of its status as a place of pilgrimage, the church was designated a minor basilica by Pope Benedict XVI on 10 August 2009.

[2][6] The architectural sources for the construction of Notre-Dame d'Alençon are to be found in churches such as La Trinité de Falaise, Saint-Germain d'Argentan, and Saint-Maclou in Rouen.

The central nave of five bays is supported by strong fasciculated columns with reduced capitals, indicative of early 15th-century construction,[2] and rising in three storeys.

[3] The middle level of the nave's elevation is a blind triforium with a lower balustrade; the broad clerestory windows are decorated with flamboyant tracery.

[2] The high altar is housed beneath a baldachin with gloria installed during the 18th-century replacement of the choir, the same era that furnished the baptismal font in the northern chapel.