Almonte was signed by the New York Yankees as an amateur free agent in 1996. He spent four years in the minors before getting called up in 2001. He made his debut on September 4, 2001. After spending the 2002 season in the Yankees minor league system, he was called up in 2003 after Derek Jeter suffered an injury, and was the team's starting shortstop until Jeter returned.
On October 31, 2007, he signed a minor league deal with the Detroit Tigers. He became a free agent after the 2008 season and signed a minor league contract with the Chicago Cubs in January 2009. He became a free agent during spring training, and the signed a minor league contract with the Milwaukee Brewers. He played the entire 2009 and 2010 seasons with the Triple-ANashville Sounds. His minor league contract was purchased by the Brewers at the conclusion of spring training in 2011. Almonte hit his first home run in nearly 10 years for the Brewers against the Reds on Saturday, April 2, 2011. He was outrighted to Triple-A Nashville on June 3, 2011.