The windows behind the alter in the sanctuary depict four of the doctors of the church: Saints Bernard, Augustine, Ambrose and Gregory. They were purchased in 1919 at a total cost of $600.00.

The large windows in the transepts represent scenes of St. Peter with the Keys to Heaven and Christ surrounded by the little children. These two windows were purchased in 1920 at a cost of $1,250.00.

Each of the side windows, in the body of the church, portray one of the eight Beatitudes. All of these windows were purchased in 1932 at a cost of $850.00 each. The order form specified "with design and color scheme to match large transept windows."

All of the stained glass windows in St. Bernard Church are insured for more than a half million dollars but are considered priceless and irreplaceable.