The settlement of New Mexico began when Juan de Oñate led a group of colonizers into the territory in 1598, serving as governor from 1601 until 1609.

Valasco replied that he had named Peralta as governor, and that Onate should hand over to him when he arrived at the Rio Grande and should then return with his son to Mexico City without delay.

Juan de Oñate had planned to move the capital south to the Santa Fe River valley.

Peralta selected a defensible site with ample available land and a good water supply for the town, which he called Santa Fe.

He and his surveyor laid out the town, including the districts, house and garden plots and the Santa Fe Plaza for the government buildings.

[10] The Palace of the Governors is now the oldest continuously occupied building in the United States, and as of 1999 housed the Museum of New Mexico.

[b][12] The church assumed that the main objective in New Mexico was to convert the Indians, and the civil power existed only in order to provide protection and to support this goal.

Perhaps to weaken the church position, Peralta issued strict regulations that imposed imprisonment for ten days by the civil authority for any Spaniard found guilty of abusing an Indian worker.

[14] Fray Isidro de Ordóñez, who had twice before been in New Mexico, arrived with the supply train in 1612 as the leader of nine Franciscan friars.

The struggle for power intensified, and in May 1613 Ordonez excommunicated Peralta, posting a notice announcing this on the doors of the Santa Fe church.

[15] On 12 August 1613 Ordóñez and his followers arrested Peralta and had him chained and imprisoned in the mission of Nuestra Señora de los Dolores (Our Lady of Sorrows) at Sandia.

[17] This was the start of long-running disputes between the friars and the secular administration, which later became so violent that in 1620 the King himself had to intervene, taking the side of his governors.

In the 1870s and 1880s James Reavis popularized the idea of a rich Peralta family who had lived and ruled over part of the American Southwest.