Trump and his wife, Melania, and Vice President Mike Pence and his wife, Karen, sat in a front pew at Washington National Cathedral for the morning service after a day of pomp, pageantry and protests that accompanied his Friday inauguration.
The interfaith service is a tradition for new presidents and is hosted by the Episcopal parish, but the decision to hold a prayer session for Trump sparked debate among Episcopalians opposed to his policies.
The service took place as throngs of women, many of them wearing bright pink, pointy-eared hats, descended on the nation's capital and other cities around the world Saturday for marches organized to push back against the new president.
Trump had no speaking role at the service.
Bishop Harry Jackson of Hope Christian Church in Beltsville, Maryland, asked God to grant the president, vice president and Cabinet members "wisdom and grace in the exercise of their duties." Jackson also asked that Trump and Pence "serve all people of this nation and promote the dignity and freedom of every person."
After church, Trump planned to visit the CIA for a meeting with members of the nation's intelligence community that could be fraught with tension.
Trump has sharply criticized top U.S. intelligence officials over their conclusions that Russia interfered in the 2016 election on his behalf, as well as over leaks about classified briefings he received in the weeks before his he was sworn into office on Friday.
Trump has signaled an intention to make a quick and clean break from the Obama administration.
Before dancing with the new first lady at three inaugural balls Friday night, Trump signed an executive order aimed at former President Barack Obama's health care law. The order notes that Trump plans to seek the law's "prompt repeal." It allows the Health and Human Services Department and other federal agencies to delay implementing parts of the law that might impose a "fiscal burden" on states, health care providers, families or individuals.
Trump also cleared the way for members of his national security team to take their places.
He signed legislation granting James Mattis, his pick for defense secretary, a one-time exception from federal law barring former U.S. service members who have been out of uniform for less than seven years from holding the top Pentagon job. The restriction is meant to preserve civilian control of the military. Mattis, 66, retired from the Marine Corps in 2013.