As result of the wars between Mexico and the Yaqui, many fled to the United States. Most settled in urban barrios, including Barrio Libre and Pascua in Tucson, and Guadalupe and Scottsdale in the Phoenix area. Yaquis built homes of scrap lumber, railroad ties and other materials, eking out an existence while taking great pains to continue the Eastern Lenten ceremonies so important to community life. They found work as migrant farm laborers and in other rural occupations.

Because of their poverty, in the early 1960s spiritual leader Anselmo Valencia approached University of Arizona anthropologist Edward Holland Spicer to help his people. A noted authority on the Yaqui, Spicer, Muriel Thayer Painter, and others created the Pascua Yaqui Association (PYA). U.S. Rep. Morris Udall, D-Ariz., agreed to aid the Yaquis in securing a land base. In 1964, the U.S. government gave the Yaqui (817,000 m²) of land southwest of Tucson, Arizona. It was held in trust for the people. Under Valencia and Raymond Ybarra, the PYA developed homes and other infrastructure at the site. Realizing the difficulties of developing the community (known as New Pascua) without the benefit of federal Tribal status, in the mid-1970s the Yaquis once again had Udall and others sponsor federal recognition legislation. The U.S. formally recognized the Pascua Yaqui Tribe based on this land on September 18, 1978. The Pascua Yaqui Tribe was the last Tribe recognized prior to the formal BIA Federal Acknowledgement Process established later in 1978.

The Yaqui have dwelt in the area of the present-day southwestern United States since before the incursions by Spanish missionaries and soldiers in the 18th century. Yaqui oral tradition and history says there were small Yaqui settlements there centuries before the arrival of Europeans. The town of Tubac,Arizona, had Yaqui in its Spanish garrison. Several communities of Yaqui have existed in Arizona since the 19th century: Pascua Pueblo is in the northwestern part of Tucson and Hu'upa was to the south. It has since been absorbed into the Valencia and Freeway neighborhood of Tucson. In addition,Marana has had continuous settlements of Yaqui.

In the late 1960s, several Yaqui, among them Anselmo Valencia and Fernando Escalante, started development of a tract of land about 8 km to the west of the old Hu'upa site, calling it New Pascua (in Spanish, Pascua Nuevo). This settlement has a population (estimated in 2006) of about 4,000 and is the center of administration for the Tribe. Most of the middle-aged population of New Pascua use English, Spanish, and a moderate amount of Yaqui. Many older people also speak the Yaqui language fluently, and a growing number of youth are learning the Yaqui language in addition to English and Spanish.

Many Yaqui moved further north, near Tempe, Arizona. They settled in a neighborhood named after Our Lady of Guadalupe. The town incorporated in 1979 as Guadalupe, Arizona. Today, more than 44 percent of the town's is Native American, and many are trilingual in Yaqui, English and Spanish.

A small Yaqui neighborhood known as Penjamo is located in South Scottsdale, Arizona. Yaqui families in California are based in Fresno. Yaquis originally residing in the border town of Presidio, Texas, who fled Sonora in 1850 after killing Mexican soldiers in a fight, are now based in Lubbock, Texas, and are known as the Texas Band of Yaqui Indians, a state-recognized Tribe under Resolution SR#989 signed by Sen. Charles Perry and the Texas state Senate.

The Texas Band of Yaqui Indians, with more than 900 members, is petitioning for federal recognition