That village in Tonalá really never settled down, for that, in the beginning of 1535 it was moved once again, now to Tlacotlán. In Tlacotán the village seemed more stable for 7 years, they were even begun to work vegetable gardens and livestock hatcheries, there was a farmers market every five days to which near populations' peasants went to sell their products. But in 1540 the calm turn into a rebellion of the indigenous towns that provoked the death of hundred of natives, leaving the village almost without inhabitants, then the Doña Beatriz's Hernández figure arose, when she decided that the village will be moved to the Valley of Atemajac with the survivors of the attack.

In February 4 of 1542, behind of the current Degollado Theater, it was carried out the ceremony of the foundation of Guadalajara, there the first city council was installed and the Emperor Carlos V of Germany and I of Spain gave it the title of City, granting it the Coat of Arms, the same one that continues representing Guadalajara until our days. In 1548 Guadalajara was transformed into the headquarters of the Bishopric, and in 1561 Brother Pedro de Ayala put the first stone of the cathedral, which will be finished by 1618. In December 10 of 1560, the Audience in Guadalajara was officially settled down, transforming this way into a capital of the Kingdom of New Galicia, a territory that include the territories that nowadays are Jalisco, Nayarit, Aguascalientes, Zacatecas, Colima and San Luis Potosí.  After the revolts and the Mexico Independence from Spain, Guadalajara transformed into Capital of the State of Jalisco in May 27 of 1824.