Many churches canceled Christmas Eve services and others went easy on Christmas decorations, The New York Times reported.
While the number of Christians still in the country has dropped sharply, exact figures are still unclear. About 500,000 remain, down from 1.4 million before the 2003 U.S.-led invasion.
More than 1,000 people may have left Iraq since the October bombing or headed to the comparative safety of the semiautonomous Kurdish area.
The Sacred Church of Jesus, home to a Chaldean Catholic congregation in Baghdad, had a tree decorated with stars. They carried pictures of the 60 people killed at the Church of Salvation.
"Yes, we are threatened, but we will not stop praying," the Rev. Meyassr al-Qaspotros said in his Christmas Eve homily.
"We do not want to leave the country because we will leave an empty space. Be careful not to hate the ones killing us because they know not what they are doing. God forgive them."