Fat Joe's first album was Represent, released in 1993, followed by Jealous One's Envy in 1995. From 1998 to 2006, he was signed to Atlantic Records, releasing four albums under the label, Don Cartagena in 1998, Jealous Ones Still Envy (J.O.S.E.) in 2001, Loyalty in 2002, and All or Nothing in 2005. Around the release of All or Nothing, Fat Joe was involved in a highly publicized feud with another New York City-based rapper 50 Cent, who attacked Fat Joe in his song "Piggy Bank". His most popular song in which he performed was "Lean Back" with Terror Squad, which was a number-one hit in the summer of 2004.
Starting in 2006, when his album Me, Myself, & I was released, Fat Joe was signed to Imperial Records, which distributes through Terror Squad Entertainment. His second album released under the label was The Elephant in the Room, which was released on March 11, 2008.
In 1995, Fat Joe released his second studio album, Jealous One's Envy, which peaked at #71 on The Billboard 200 and at #7 on Top R&B/Hip Hop Albums. The album featured a guest appearance from KRS-One and production from Diamond D. The lead single was "Success", which did not chart, but his second single, "Envy" peaked at #8 on the Hot Rap Tracks chart. The success of this album led Fat Joe to be featured on the remix of LL Cool J's single "I Shot Ya" along with Foxy Brown, Keith Murray and Prodigy of Mobb Deep.
Joe himself acknowledged, in an interview with HipHopGame.com, that he has received criticism for releasing only one solo album by a former Terror Squad member, Remy Ma, as well as barely featuring original members Prospect and Armageddon on "True Story." Terror Squad singer Tony Sunshine has had possible album release dates pushed back over three years, and Joe had stated that artists Prospect and Armageddon have not released solo albums yet as the result of them being "really lazy". Former Terror Squad member Triple Seis also went on record when asked who had written Fat Joe's lyrics, stating that he and Pun were Joe's ghostwriters, and asserts that Joe continues to hire ghostwriters.
Fat Joe released his fourth album Jealous Ones Still Envy (J.O.S.E.) in 2001, featuring production from the then-popular Irv Gotti. The album featured a star-studded line up from the likes of Ashanti, Ja Rule, N.O.R.E., Busta Rhymes, Petey Pablo, M.O.P., Ludacris, R. Kelly, Buju Banton, and artists from his Terror Squad label. The lead single "We Thuggin'" featuring R. Kelly was a big hit in late 2001, but would not reach the level of the Irv Gotti-produced "What's Luv?" which was a massive hit in early 2002 and featured Murder Inc. superstars Ja Rule and Ashanti. The album was Fat Joe's biggest hit as it was successful from its January release all the way into May, being certified platinum. However, Fat Joe's fifth album Loyalty, out in 2002 and featuring production from Irv Gotti, was not as successful.
In 2003, Fat Joe was featured in the pop single "I Want You" by Mexican singer Thalía. The same year, he and Tony Sunshine performed the single "Crush Tonight" from Loyalty on the Comedy Central program Chappelle's Show, hosted by comedian Dave Chappelle.
Despite the setback, Fat Joe scored a number-one hit in 2004 with his group Terror Squad, collaborating with Remy Ma on the Scott Storch production "Lean Back" from the album True Story. The song was criticized twice by conservative columnist L. Brent Bozell III for its extensive use of obscene language. However, Jason Birchmeier of Allmusic called the song "a perfect club-ready duet between Joe and Remy that boasts a trademark Scott Storch beat and a memorable singalong hook (and dance-along step)".
Three years later, in 2005, Fat Joe released his sixth album All or Nothing, noted for featuring the popular diss track "My Fofo" aimed at fellow New York rapper 50 Cent, who had dissed Joe for recording with Ja Rule. All or Nothing spawned the singles "So Much More" and "Get It Poppin" featuring Nelly, also with guest appearances from Eminem, Mase, Remy Ma, Mashonda, and R. Kelly. Responding to "My FoFo", 50 Cent attacked Fat Joe in his 2005 song "Piggy Bank" from his album The Massacre. Fat Joe, subsequently, attacked 50's street credibility and called him a "coward" on a phone interview with Kay Slay of New York City hip-hop radio station WQHT. Fat Joe also released a track criticizing 50 Cent in his 2005 album All or Nothing titled "My FoFo" (referring to his .44). The conflict carried on at the 2005 MTV Video Music Awards, while Fat Joe introduced the reggaeton act featuring Daddy Yankee, Joe remarked, "I feel safe with all the police protection—courtesy of G-Unit. Shortly after, when MTV switched to a commercial break, 50 Cent directed an obscenity at Joe, and 50 Cent jumped on stage as Fat Joe was leaving.
In June 2007, the Reverend Michael Pfleger targeted Fat Joe as among several rappers he believed promoted misogyny in his billboard campaign "Stop Listening to Trash", which was launched June 18, 2007 throughout Chicago, Illinois, where Pfleger preaches. Also that month, Fat Joe was featured in the DJ Khaled single "We Takin' Over", from the album We the Best, alongside several other performers. In September 2007, on the BET program Rap City, 50 Cent again criticized Fat Joe, who responded in early January 2008 on Rap City that 50 Cent's criticism was nonsense and that he was just trying to re-introduce the earlier feud from 2005 from 50 Cent's song "Piggy Bank". Later in January, 50 Cent released another Fat Joe diss, called "Southside Nigga (I'm Leaving)". At the end of January 2008, Fat Joe and his longtime accountant Brian Dittrich both denied rumors spreading on the Internet that Fat Joe owed the IRS in taxes.
Fat Joe's eighth solo studio album The Elephant in the Room was distributed by Imperial Records, a division of Capitol Records and Terror Squad Entertainment, and released on March 11, 2008; its lead single was "I Won't Tell" featuring singer J. Holiday. The album debuted at the sixth position on the Billboard Hot 100.
On March 20, 2008, shortly after record sales were released for Fat Joe's new album The Elephant in the Room, 50 Cent released a video via online, which features the "funeral" of Fat Joe, which shows 50 Cent crying in the fake footage. 50 Cent then talks about Fat Joe's record sales, and states that he ended Fat Joe's career (like he says he did to Ja Rule's) and that his mixtape blew out Fat Joe's album. In April 2008, Fat Joe hosted a mixtape by KAR Mafia (Kill All Rats Mafia) called "Gay Unit Volume 1". You Ain't Sayin' Nothin', the CD's second single, was released in April 2008 as a single.