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By this time, the Yaqui people had suffered greatly. Many Yaquis left the Rio Yaqui area to fight in the Vakatetteve Mountains; others relocated to Yaqui communities in Arizona. Many more died in battles or were executed. In 1868, 600 Yaqui men, women, and children were captured near Vahkom Pueblo by Mexican state and federal troops. Their arms (bows and arrows and rifles) were taken, and 450 were locked in a church. During the night, the church was shelled. 120 of the people inside were massacred. But still, the Yaquis continued to believe in and fight for the right to land, autonomy, and freedom from harassment.

The Mexican government tried various tactics to defeat the Yaquis. Many were killed. Mexican troops would occupy Yaqui pueblos to keep watch over them. Yaquis were also deported to work as slaves in many distant areas of Mexico, as Yucatan, Oaxaca, Vera Cruz, Mexico City, and Guadalajara. The deportation of Yaquis extended past the borders of Mexico to include Bolivia, the islands of the Caribbean, and the United States.

The Yaquis continued to resist subjugation. By 1887, the Mayo tribe had stopped fighting. Smallpox disease had killed off many members of the Yaqui tribe so that only 4,000 Yaquis remained in the Rio Yaqui area. There were yet Yaqui who continued to battle the Mexicans. These were led by Cajeme, meaning "He Who Does Not Drink", and Juan Maldonado, who was also called Tetabiakte, "Rolling Stone". The Yaquis in Arizona sent guns and supplies to help the battle.

Significant Yaqui relocation occurred from the United States to Sonora and from Sonora to the United States during the 1880s. In 1897, a peace treaty was signed at Ortiz, Sonora between the Yaqui people and the Mexican government. But, after two years, war and deportation of Yaquis continued.

Yaqui families lived in the Gila and Santa Cruz River valleys since time immemorial. Around the turn of the century, these families, encouraged by farmers, politicians, and internal preferences, began moving into larger communities. Guadalupe took early form in 1880. Old Pascua Village was established in 1903. The Sonoran Governor Izabal had a policy to arrest and deport both peaceful and rebel Yaquis. This forced Yaquis to relocate to the Arizona communities and to join old family groups already in residence. Many Yaqui families moved to escape the violence of the 1910-1920 Mexican Revolution.

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