After the annexation of Texas by the United States in 1845, he was elected to the U.S. Senate together with Thomas Jefferson Rusk. Houston served there from February 21, 1846 until March 4, 1859. He was considered a potential candidate for president. But, despite the fact that he was a slave-owner, his strong Unionism and opposition to the extension of slavery alienated the Texas legislature and other southern States, especially with his support of the Oregon Bill (1848) and the Compromise of 1850 and his opposition to the Kansas-Nebraska Act. He was a lame duck senator from 1857.
He ran for governor of Texas, unsuccessfully in 1857 and successfully in 1859, making him the only person in U.S. history to be the governor of two different states. He resigned in March 1861 following his refusal to take an oath of loyalty to the Confederacy. He was replaced with Edward Clark, having refused the use of force to prevent the secession.