The sanctuary of Second Presbyterian Church is widely regarded as one of the best Arts and Crafts interiors in the nation. Howard Van Doren Shaw's bold architecture is enhanced by thirteen Frederic Clay Bartlett pre-Raphaelite murals and a phenomenal collection of stained glass windows by Louis Comfort Tiffany, Edward Burne-Jones, Louis Millet, and others. Tiffany's large 1903 Peace Window was completely restored in 2018. Every design element from Shaw's 1901 re-building of the interior (following a devastating fire in March 1900) is still in place: carved wood panels, molded plaster angels, ceiling grotesques, beautiful unique light fixtures, a grape and vine light screen, original Arts and Crafts carpet, and more. Architect James Renwick Jr.'s Gothic Revival exterior features a unique, mottled limestone.

Docents are available to give free tours during public tour times: Wednesdays from 1:00 p.m. to 3:00 p.m., Saturdays from 11:00 a.m. to 3:00 p.m., and Sundays at 12:15 p.m. Group tours are available upon request.