General manager Jeff Luhnow says the decision wasn't based on Houston's record but because "we need a new direction in our clubhouse."
The Astros entered Monday in fourth place in the AL West with a 59-79 record, second worst in the league.
"Bo's passion and energy are unparalleled, and his desire to win unquestioned," Luhnow said in a statement. "This decision was not made because of our current level of competitiveness in the Major Leagues. I recognize that our win-loss record is largely a product of an organizational strategy for which I am responsible.
"... What we will seek going forward is a consistent and united message throughout the entire organization. It is essential that as an organization we create an atmosphere at the Major League level where our young players can come up and continue to develop and succeed. Ultimately, I am responsible for creating that culture, and I will do everything in my power to do so-even when it means making difficult moves like the one we made today."
Bench coach Dave Trembley was also let go and Tom Lawless takes over as interim manager. Lawless worked in Houston's minor league system and was the interim manager at Triple-A Oklahoma City this season when manager Tony DeFrancesco was on medical leave.
Porter joined the Astros for the 2013 season after working as a third base coach for the Washington Nationals.
"This was not an easy decision to make," owner Jim Crane said in a statement. "We wish Bo nothing but the best in the future. Jeff has my full support moving forward. Our goal to bring a championship to Houston remains."
Adam Everett, who was also working in the minors, will replace Trembley.
The Associated Press contributed to this report.