After signing with the Rays, Longoria tore through his first assignments in the minor leagues. In 2006, after just eight games with the short season Single-A Hudson Valley Renegades, Longoria was promoted to the Visalia Oaks and impressed the organization with his quick success, hitting .327/.402/.618 with eight home runs and 28 RBIs in 28 games. This earned him a promotion to the Double-A Montgomery Biscuits, where he hit .267/.266/.486 with six home runs through the end of the season, and hit .345 in the postseason, including a walk-off two-run home run in the Southern League Division Playoffs to put Montgomery into the championship. He was the 2007 Most Valuable Player with the Biscuits as well as a postseason all-star. On top of that he won a player of the week award. He was widely considered the top third base prospect in the minors and one of the top prospects at any position.