Like Abó, it took until the 1800s for people to resettle the area around Quarai. Miguel and Juan Lucero and their families were the first to move back to Quarai in the early 1820s. At this time the remains of the Quarai church and convento were still in fair condition, and the Lucero families moved into rooms of the convento. The Luceros cleaned out a number of the rooms, patched the walls, and fixed the still remaining roofs. Later, rooms were added, and new houses were built from the mission rubble. A large wall encompassed the new buildings for added protection.
Unfortunately, like the reoccupation of Abó, there was an increase in Apache raids around 1830. This time, the Apaches burned the Quarai church and convento, causing the remaining roof to collapse, and destroyed much of what the Lucero family had built. This led to the second abandonment of Quarai.
Some of the Lucero family returned in the 1840s, constructing new structures including a torreon southeast of the mission. Miguel Lucero sold the land to Bernabe Salas in 1872, but this was short-lived as Salas abandoned the Lucero structures and moved to the nearby town of Punta de Agua by 1882. The remains of these structures are still visible today along the Quarai interpretive trail.