Apart from official colonial settlements ("villas"), population centers in Guanajuato were either congregated around a Church mission or were native villages. In the seventeenth century, none of these had yet shown any noteworthy development. Silao was an insignificant hamlet of barely 24 houses inhabited by a few Spanish, Spanish-Indians, mulattoes and natives, along with around 50 Spaniards and 260 natives who lived on the haciendas.

The Congregation of Irapuato consisted of just 12 Spanish houses plus another 10 or so married natives, along with a workforce of some 300 married natives and a few slaves. In Apaseo, there were around 400 natives, although these were shared with another village called Aguas Calientes. Today Apaseo el Grande, at the time it was the Apaseo Farm and was dedicated to wheat production.

The seventeenth century was a period of rural development. The village of San Luis de la Paz consisted of a few Spaniards plus 80 natives. San Miguel had around 70 Spanish and Spanish-Indians, 50 natives and a few mulattoes. In the Villa of San Felipe, there were just seven Spaniards and four natives. In the Bajio region, the situation was different: The Villa of Celaya had a population of 200 Spanish and 2,500 natives; San Juan had 50 and San Miguel 10. In the Villa of Leon, there were 75 married Spaniards, with 12 widows and 12 bachelors. Villages such as Coecillo and San Miguel were populated by small groups of 10 or 12 natives made up of a mixture of Mexicas, Otomis and Purepechas. On the farms, ranches and haciendas of the parish, there were between one and ten natives working at any one time.

New towns were born, such as the Villa de Salamanca on the lands of the ranches of Valtierra and Barahona. Sanchez Torrado chose the area because of the proximity of the Rio Grande, drawing water off by means of irrigation ditches and reservoirs. The Viceroy made it a condition that, on reaching a population of 30 married men, a civil leader should be elected, along with four councilors and two magistrates.

Around the middle of the century, the city of San Andres was founded in Salvatierra, where there were already 40 Spaniards and their families.

The Congregation of San Pedro Piedra Gorda has a different history. In 1680, several ranchers who lived in different parts of the valley got together to found the Brotherhood of Jesus of Nazareth. However, the organization lacked land, so Juan Montañez bought a portion of land from Nicolas Galvan de Rojas and in March, 1681 the Congregation of Valle Florido or Piedra Gorda was established. Other towns in the area were founded by the native population, such as San Francisco and Purisima del Rincon, to the southwest of Leon.