In a similar way to Abó, it wasn't until the 1800s that people began to move back to the area around Quarai. In the early 1820s, Miguel and Juan Lucero, along with their families, were the first to return to Quarai. At that time, the ruins of the Quarai church and convento were still in decent shape, so the Lucero families settled into some of the convento's rooms. They worked hard to clean out several rooms, repair the walls, and fix the roofs that were still intact. Eventually, they added more rooms and built new houses using materials from the mission's ruins. A large wall was constructed around the new buildings for extra security.
Sadly, just like what happened in Abó, there was a rise in Apache raids around 1830. The Apaches attacked Quarai, setting fire to the church and convento, which caused the remaining roof to fall in and destroyed much of what the Lucero family had worked to build. This resulted in Quarai being abandoned once again.
Some members of the Lucero family came back in the 1840s and built new structures, including a Torreon to the southeast of the mission. In 1872, Miguel Lucero sold the land to Bernabe Salas, but this arrangement didn't last long. By 1882, Salas had left the Lucero buildings behind and moved to the nearby town of Punta de Agua. Today, the remnants of these structures can still be seen along the Quarai interpretive trail.