The motto IN GOD WE TRUST was placed on United States coins largely because of the increased religious sentiment existing during the Civil War. Secretary of the Treasury Salmon P. Chase received many appeals from devout persons throughout the country, urging that the United States recognize the Deity on United States coins.

http://www.treas.gov/education/fact-sheets/currency/in-god-we-trust.shtml

Another Act of Congress passed on March 3, 1865. It allowed the Mint Director, with the Secretary’s approval, to place the motto on all gold and silver coins that “shall admit the inscription thereon.” Under the Act, the motto was placed on the gold double-eagle coin, the gold eagle coin, and the gold half-eagle coin. It was also placed on the silver dollar coin, the half-dollar coin and the quarter-dollar coin, and on the nickel three-cent coin beginning in 1866. Later, Congress passed the Coinage Act of February 12, 1873. It also said that the Secretary “may cause the motto IN GOD WE TRUST to be inscribed on such coins as shall admit of such motto.”

The use of IN GOD WE TRUST has not been uninterrupted. The motto disappeared from the five-cent coin in 1883, and did not reappear until production of the Jefferson nickel began in 1938. Since 1938, all United States coins bear the inscription.