Moeller attended the University of Southern California (USC). In 1996 he was an All-Pac 10 selection and from 1994 - 1996 was teamates with former Reds infielder, Aaron Boone. He would go on to get drafted in the 7th round of the 1996 Amateur Draft by the Minnesota Twins.
When he was with the Brewers, Moeller was used increasingly only for calling games with staff ace Ben Sheets. He did however Hit for the cycle on April 27, 2004. He was the first to do it at home, and the first since Paul Molitor did it on May 15, 1991 at Minnesota.
In January 2006, Moeller was named to the USA's provisional roster for the 2006 World Baseball Classic.
Just prior to the 2006 All-Star break, Moeller was designated for assignment by the Brewers, primarily due to his low .184 batting average. After clearing waivers he joined the AAA Nashville Sounds. He was replaced with Mike Rivera by the Brewers. Moeller began the 2007 season with the Cincinnati Reds. After splitting time between Cincinnati and the AAA Louisville Bats, he was traded to the Los Angeles Dodgers for cash considerations on August 11, 2007.
On November 27, 2007, Moeller signed a Minor League contract with an invitation to spring training with the Washington Nationals. He was released by the Nationals on March 10, 2008, and signed a minor league contract with the New York Yankees the same day. The Yankees purchased his contract on April 14 following injuries to Jorge Posada and José Molina. He made his first appearance as a Yankee against the Tampa Bay Rays that night, going 1-4. In an April 16 victory over the Boston Red Sox, Moeller went 3-4 with a double and an RBI, notching his first 3-hit game since July 22, 2004. On April 25, 2008, Moeller was designated for assignment to make room for Jonathan Albaladejo and Chris Britton after Brian Bruney was placed on the 15-day Disabled List and it had been thought that Posada was going to be able to play. On April 30, after clearing assignment waivers, the Yankees added Moeller back to the active roster, due to the injury to Posada.Played third and first base twice in 2008 for the first time in his career.