Born in Rio Piedras, which is located in San Juan, Puerto Rico, to John Lee Bottom and Arlyn, Joaquin moved to the United States when he was very young. His family, who had ceased to practice Christianity, joined a cult order Children of God, and moved around frequently to various places in South America. After being disillusioned with their religious group, his parents decided to part ways with the cult and decided to start afresh in the US. To mark the new beginning to their lives, his family chose the last name 'Phoenix'. Joaquin, the third among five siblings, wanted to have a nature-related name like his siblings, and chose to call himself Leaf.
To support his family financially, Joaquin, along with his other siblings, sang and performed in various talent shows and contests. Irish Burton, one of Hollywood's leading child actor agents, noticed the flair and confidence in the five children and offered them roles in several commercials and television shows. As a child actor he used the name Leaf, but at the age of fifteen he chose to be called Joaquin.
He made an appearance along with his brother River in the American Musical Television series Seven Brides for Seven Brothers in 1982, and joined him in a TV series about dyslexia called Backwards: The Riddle of Dyslexia. He made an entry into the world of the big screen in 1986 with the movie Space Camp, which received a lukewarm response. His first major role, in which he donned the character of Danny in the movie Russkies, came in 1987. On October 31, 1993, a drug overdose claimed the life of his brother River, just outside the popular nightspot The Viper Room, owned by Johnny Depp. Joaquin's frantic calls to 911 were televised incessantly on television channels. The constant scrutiny of the media took an emotional toll on Joaquin and he decided to quit his acting career.
With the constant coaxing of his friends, he reemerged onto the movie scene in 1995, being cast opposite Nicole Kidman in the movie To Die For, in which he played the role of a troubled teenager. His performance as a troublemaker in a small town in the movie U-Turn, directed by acclaimed director Oliver Stone, earned him accolades from movie lovers the world over. In 2000, his depiction of the cruel emperor Commodus in the movie Gladiator, directed by Ridley Scott, earned him a nomination for Best Actor in a Supporting Role at the Academy Awards. His impressive performance in the movie Signs, directed by M. Night Shyamalan, resulted in him being cast in the 2004 film The Village, directed by the same director.
In 2005, to get into the character of Country legend Johnny Cash, whom he was going to portray in the movie Walk The Line, Joaquin bought himself a guitar and practiced to step into the shoes of the charismatic singer. The result was five nominations at the Academy Awards, including one for Best Actor. He won a Golden Globe in the same category for his performance in that movie. He recorded the soundtrack of the movie Walk The Line, which won a Grammy for his outstanding work on the album. On October 27, 2008, he made a formal announcement about retiring from movies to concentrate on his music career as a rapper.
Apart from his exploits as an actor, Joaquin has directed videos for bands such as People in Planes, Ringside, and Arckid. He has also served as a producer on the movie We Own the Night and has been one of the executive producers on the TV show 4Real. He actively participates in campaigns organized by PETA.