On June 28, 2007, Biggio became the 27th player in the history of Major League Baseball to join the 3,000 hit club, with a single against Colorado Rockies pitcher Aaron Cook. Though Biggio was tagged out on the play attempting to stretch it into a double, drawing the throw allowed a run to score. The game action paused while Biggio shared the moment with his wife and children. Longtime friend and former teammate Jeff Bagwell emerged from the Astros clubhouse to congratulate him. Biggio became the first player in Astros history to accumulate 3,000 hits. It was Biggio's third hit of the game, and he went on to accumulate two more later in the game, one in the ninth inning and one in the eleventh inning. Biggio's 3,000th hit came on the same day that Frank Thomas hit his milestone 500th career home run, both marks which are considered to guarantee one's induction into the Hall of Fame.
On July 24, 2007, Biggio announced his retirement, effective at the end of the season (his 20th season with the club, a franchise record). Hours later, with the Astros locked in a 3–3 tie with the Los Angeles Dodgers, Biggio hit a grand slam in the 6th inning. The Astros went on to win the game 7–4.
A sellout, record-breaking crowd packed Minute Maid Park on September 30, 2007, to witness Biggio's final game. He recorded his final career hit, a double in the first inning, and scored his final career run that same inning. In his final career at-bat, he grounded the ball to third baseman Chipper Jones, who threw out the hustling Biggio by half a step. He left the field to a standing ovation from the fans, and when he was replaced defensively in the top of the 8th inning he shook hands with umpires and teammates and left to another standing ovation as he waved to the fans. The Astros won the game 3–0.
Biggio has received awards from various organizations, including the Hutch Award (2005) and being named one of Sporting News' Good Guys (2004). The Hutch Award is given to a player that shows competitiveness and never gives up. Part of the reason Biggio was given the award was for his multiple position changes, but also because of his work in the community and inspiring other teammates to participate as well. He also received the Roberto Clemente Award in 2007. The Roberto Clemente Award "recognizes the player who best exemplifies the game of baseball, sportsmanship, community involvement and the individual's contribution to his team".