The confrontation had been building since 1595, when King Philip II of Spain granted conquistador Juan de Onate permission to colonize New Mexico. By 1598, Onate's plans were clear to the Acoma: the Spanish intended to force all Pueblo peoples into new valley settlements under colonial rule, subject to the encomienda labor system and mandatory Catholic conversion. Zutacapan, the Acoma cacique and spiritual leader, prepared to resist. When Onate's nephew Juan de Zaldivar arrived at the pueblo on December 4, 1598, demanding food and shelter for himself and sixteen soldiers, the Acoma refused. The Spanish reportedly broke into homes, seizing maize and blankets by force. A fight erupted, and Zaldivar and eleven of his men were killed. The Acoma had drawn a line, and Onate would answer with overwhelming violence.

Onate dispatched Zaldivar's brother, Vicente de Zaldivar, with about seventy soldiers. They arrived at Acoma on January 21, 1599. The next morning, the assault began. For two days, the Acoma held their ground against the Spanish forces, their mesa-top position providing a formidable defensive advantage. On the third day, Zaldivar devised a plan to breach the defenses. He and twelve men scaled the mesa walls and opened fire with a cannon. The heavy artillery overwhelmed the Acoma's arsenal of war clubs, spears, and darts. A large fire engulfed many homes during the fighting. At the time, an estimated 4,000 people lived at or around the pueblo, including at least 1,000 warriors. The three-day onslaught killed roughly 800 men, women, and children. Around 500 survivors were taken prisoner.

Onate held a trial at San Juan Pueblo and handed down punishments calculated to crush resistance across the region. Every Acoma male over twenty-five was sentenced to have his right foot cut off and to serve twenty years of enslavement. Twenty-four men suffered the amputation. Males between twelve and twenty-five, along with all females over twelve, were enslaved for the same period. Most prisoners were parceled out among government officials and Franciscan missions. Sixty of the youngest women were sent to Mexico City and distributed among Catholic convents. Two Hopi men, captured at the pueblo, each had a hand severed and were released to spread word of Spain's power. The severity was deliberate: Onate intended the punishment as a warning to every pueblo in New Mexico.

The cruelty was too much even for the Spanish Crown. When King Philip learned what Onate had done, he banished the conquistador from New Mexico. Onate returned to Spain to live out his remaining years. But for the Acoma, the damage was done. Several people escaped capture during the attack, and by 1601, just two years after the massacre, they had rebuilt their pueblo on the same mesa. That rebuilt settlement still stands today, a testament to the resilience of the Acoma people. The community has endured through centuries of colonial occupation, disease, and cultural suppression, maintaining their language, ceremonies, and identity on the mesa where their ancestors chose to make their stand.

The massacre remains a raw nerve in New Mexico. In 1998, on the 400th anniversary of Spain's founding of the colony, a group of Acoma people cut the right foot off an equestrian statue of Juan de Onate in Alcalde, New Mexico. They issued a statement: 'We took the liberty of removing Onate's right foot on behalf of our brothers and sisters of Acoma Pueblo.' The foot was replaced that same year. In 2007, when an even larger bronze equestrian statue of Onate was erected in El Paso, Texas, Acoma tribal members protested at the dedication ceremony. In June 2020, both the Alcalde statue and another Onate monument in Albuquerque were removed during protests following the murder of George Floyd. The debates over these monuments reveal how the events of January 1599 continue to shape conversations about memory, justice, and whose stories are told in stone.