After the Battle of Gonzales, he helped organize Texas's provisional government and was selected as the top-ranking official in the Texian Army. He led the Texan Army to victory at the Battle of San Jacinto, the decisive battle in Texas's war for independence against Mexico.
After Texas joined the Union in late 1845, Houston headed back to Washington as one of the new state's two U.S. senators. In the Senate from 1846 to 1859, he made a name for himself as a staunch Unionist in an era of increasing sectional tensions over the issue of slavery.