John LaFarge designed the seventeen stained glass windows in Judson Memorial Church, a project that illustrated the artistic unity of all the windows to each other and to the structure as a whole. The importance of stained glass windows to complement the complete architecture is evident on the architect’s earliest plans. The opalescent glass windows "translate the Italian Renaissance niche sculptures into pictorial stained glass" (Sloan 300-309). LaFarge designed the colors and textures of the windows to imitate the effect of sculpted marble and stone. Juliet Hanson, LaFarge’s assistant, painted images on thousands of pieces of glass leaded together, and the effect is nearly photographic. LaFarge designed one large rose window, three tondi, or circular, windows, a square window on the stairwell leading to the sanctuary and twelve oblong windows at regular intervals along the interior walls.

In the north facade wall, this window of the Apostle Peter, completed in 1892, measures 15 by 5 feet. The three windows of the facade wall depict Peter, Paul and John the Evangelist and each memorialize distinguished Baptist leaders of the nineteenth century.

The Centurion at Prayer measures 14 feet, six inches by 4 feet, six inches and resides in the east wall. LaFarge finished this adaptation of an engraving of a fifteenth century lost mural in 1908. It commemorates James Knott, proprietor of the Judson Hotel.

Angel in Adoration is a tondo, one of Judson’s round windows with a diameter of 54 inches. It was completed in 1892 and is positioned on the stairwell into the sanctuary. The features are that of LaFarge’s assistant and mistress.