Designed by architect Alexander Rice Esty and constructed in 1861, it was the first building completed on Newbury Street in Boston's newly filled Back Bay.

In 1899, Frederic Crowninshield designed its sanctuary's centerpiece window, in which the allegorical figure Piety, from John Bunyan's The Pilgrim's Progress, points the way to Emmanuel's Land.

An all-encompassing product of and testimony to the artistry of Ninian Comper, the work comprises a decorative scheme for the chapel designed by the architectural firm of Allen & Collens.

The chapel memorializes Leslie Lindsey and her husband of ten days Stewart Mason, who were married at Emmanuel Church and perished when the Lusitania was torpedoed in 1915.

Its outreach program in the early twentieth century, known as the Emmanuel Movement, was influential in the development of self-help groups for mental health, particularly for alcoholism.