Juan was the long-lost son of lovebirds Miguel Morez and Lily Rivera. Lily had gotten pregnant with Juan at the age of sixteen and Lily's crime boss father, Hernando, had forced her to give Juan up for adoption when he was an infant. Hernando put a hit on Miguel and his family smuggled him out of Puerto Rico. Due to this, Lily believed that Miguel had died. However, they were reunited in 1994 when Sonny Corinthos located Lily and brought her to Port Charles, where Miguel was living at the time. Lily and Miguel were still very much in love.
Lily and Miguel began searching for Juan, who was six years old at the time, in Puerto Rico. When they did find him, they learned that he was adopted by a loving family and they were elated that Juan was happy.
In 1999 a runaway Juan arrived to Port Charles believing that Sonny was his father. Sonny was married to Lily when she died a tragic death in 1996. Sonny feared that Juan would get mixed up in his mob life, so he tried pushing Juan away for his protection. Later on, Sonny revealed that Miguel was Juan's real father and the two made peace.
When Juan and Emily Quartermaine met eachother, they were instantly captivated by one another and waged a war against the Quartermaines and Juan's adoptive father to stay together. They won their war and Juan's father agreed to let him remain in Port Charles with Lieutenant Taggert as his guardian. After a while, Emily discovered that Juan had an amazing voice and urged him to pursue a singing career at her cousin Ned's record company, L&B Records. Juan was reluctant at first, but he began to warm up to the idea and even sang a number with Emily and Elizabeth Webber at the 2000 Nurses Ball.
After the Nurses Ball, Alison Barrington, granddaughter of the wealthy, well-to-do Amanda Barrington, began to develop eyes for Juan. She invited him to a rave that was being held in an old, abandoned house. Even though she didn't want to go, Emily went with Juan to the rave, along with Elizabeth Webber, Lucky Spencer, and Nikolas Cassadine. While there, Emily and Juan got into a big fight and then Juan went off with Alison and left Emily alone. As she was walking into another room, she caught sight of Alison and Juan kissing! Since she was upset enough already, she accepted a beer that was offered to her, but little did she know, the beer was drugged. She then began talking to a guy named Ted and eventually, he suggested that they leave the rave and go somewhere quieter. The next morning, Emily woke up naked in a motel room with a drug needle in her hand. Ted was next to her, but he was dead. Fortunately, Lucky showed up soon after. He had tracked her down at the motel by asking people at the rave if they had seen anything. After taking Emily to Elizabeth, Lucky and Nikolas got Ted's body and put it in a freezer in the basement of Nikolas' uncle's mansion on Spoon Island. Juan tried comforting Emily during this crisis, but Emily couldn't get past his flirting and kissing with Alison. It was ultimately revealed that Ted was a undercover cop who wanted to help Emily. Zander Smith had set Emily up to be drugged, but his boss, Joseph Sorel, was responsible for Ted's death.
Zander kidnapped Emily and fled Port Charles. At the Canadian border, Emily began realizing that Zander wasn't all that bad. When they returned to Port Charles, Zander was taken to jail at the PCPD, but Emily visited him everyday. During all of this, Juan began to get jealous. They hadn't really been a couple since before Emily was kidnapped, but Juan wanted her back and had apologized profusely for his mistakes and told her that he loved her. Not only had he kissed Alison, but Emily had also caught him with Alison's friend Sherry. Finally Emily decided that she would rather be with Zander, and so when Juan forced her to choose, she told him it was over.
In 2001 Juan decided to go on a tour to South America and asked Taggert for permission to leave. Taggert was sad to see Juan leave town, but gave him luck. Before leaving, Juan and Emily shared a tender good-bye. After Emily left, Juan whispered that he still loved her. Juan left town, and hasn't been heard from since.
Juan left town and was not heard from again for several years until his cousin Sabrina Santiago moved to Port Charles. Elizabeth contacted Juan after Sabrina became engaged and asked him to deliver the dress Sabrina's mother had worn on her wedding day to Port Charles. Juan was unable to stay for the wedding but he wished his cousin well and briefly visited with Elizabeth. During their chat, Juan revealed that he was still a musician and that he was married to a woman named Becky.
Juan returned to see his cousin after the unexpected death of her infant son. He attended the funeral with Sabrina and offered to spend some time with her in Puerto Rico while she mourned the death of her child. Sabrina appreciated the offer and they left after the funeral.