In 2000 he was elected president in a three-way race, succeeding Lee Teng-hui and ending more than 50 years of KMT rule. The DPP did not control the legislature, however, restricting Chen's ability to enact reforms. Chen had long called for Taiwan's formal independence from China, a step the mainland has said would lead to military action, but moderated his position prior to the campaign. The issue, nonetheless, remained a source of tension with China, as Chen has continued to support such a move during his terms president.

Chen was reelected in 2004; in the final days of the campaign he was wounded in an apparent assassination attempt that opposition leaders accused him of staging. In the second half of 2006 a series of corruption accusations and indictments against Chen and his family led KMT legislators to attempt to remove Chen from office three times, but each time the party failed to achieve the two-thirds vote required to do so. Chen resigned as DPP party leader in Jan., 2008, when the KMT won a landslide victory in the legislative elections. Beginning in Dec., 2008, after Chen had left office, he and his wife were indicted on corruption charges, and were convicted and sentenced on several corruption and other charges in 2009, 2010, and 2011.