The city was founded in 1542, but it was not until March 8, 1826 that it was properly granted the title of city, in the year of 1926 it was declared a historic monument by the Mexican government, since then, the development of the historic district is restricted to preserve the colonial character of the town.

In 2002 it was declared a magical town,  but the title that withdrawn 6 years later because on July 7, 2008 it was registered by UNESCO as a cultural heritage of humanity under the name of Villa Protectora de San Miguel and Sanctuary of Jesus Nazareno de Atotonilco. The distinction was granted for the cultural and architectural contribution to the Mexican Baroque and its importance in the struggle for Mexican independence. 

In the years 2017 and 2018 it was named by Travel + Leisure as the best city in the world for its quality service, friendliness, gastronomy, cleanliness, shopping experience and mobility as well as its great cultural contribution, architectural beauty and places of interest and fun, being the only city in Latin America that has managed to be number one for two consecutive years.