The first council built its first town hall in 1576, on the same site where the Government Palace is now located.

It is known that during the 17th century and the first quarter of the 18th century, the construction underwent considerable improvements. The adobe of the walls was replaced with quarry and the thatched or tile roof with solid earthenware.

In 1775, the architect Nicolás de Láfora design a new building, and it was completed in 1783. Unfortunately, the earthquakes of 1787 and 1801 damaged the work.

The entire building is made of green quarry. The large, very detailed stairway mural (1980), by Arturo García Bustos, depicts famous Oaxacans and Oaxacan history, including Benito Juárez, José María Morelos, Porfirio Díaz, Vicente Guerrero and the 17th-century nun and love poet Juana Inés de la Cruz.