After Texas readmitted itself to the Union in April 16, 1870, Houston was going to grow during the reconstruction era. Houston became a port of entry on July 16, 1870. Its new charter drew up eight wards. Many freed slaves opened businesses and worked under contracts. The Freedmen's Bureau stopped abuse of the contracts in 1870. Many African-Americans at the time were in unskilled labor. Many former slaves legalized their current marriages after the American Civil War. African-American pupils were taught in separate facilities from Caucasian children. Soon after the Reconstruction, Jim Crow laws arrived in Houston.

Lumber became a large part of the port's exports, with merchandise as its chief import. The Houston Post was established in 1880. The Houston Chronicle followed on August 23 of that year. Former U. S. President Ulysses Grant came to Houston to celebrate the opening of the Union Station, which had rail links with New Orleans. Fifth Ward residents threatened to secede from Houston because they felt they already had been separated. An iron drawbridge built in 1883 pacified them, and they did not secede. In 1887, the Sisters of Charity of the Incarnate Word established a hospital that would become Saint Joseph's Hospital.

In 1893, George H. Hermann donated a site for the purpose of a charitable hospital, which would later become Memorial Hermann Hospital in the Texas Medical Center. In 1898, Houstonians appealed before Congress for permission to turn the Buffalo Bayou into a deepwater port, prompted in part by the Spanish-American War; construction of the Port of Houston was approved by Congress in 1899.