The church needed a larger facility and began construction on what is now the main sanctuary. The initial service in that building, built longside the first, was held on Easter Eve, 1859. The original structure was razed in 1878. In 1992, the federal government designated the present building a National Historic Landmark.
The structure is a fine example of American Gothic ecclesiastical styles of the 15th and 16th centuries. A 151-foot spire, pointed arches, and ribbed vaults distinguish the church. Stained glass tracery windows bring natural light into the nave and aisles.
In 1946, the organ, built by the American firm Aeolian-Skinner, was installed at the Church of the Nativity. A beautiful example of the Aeolian-Skinner company's voicing and overall superiority of tonal design, the organ fits beautifully into the church's overall aesthetic and acoustics.