Khalifa spent the 1984 season with the Nashua Pirates of the Eastern League in 1984. He batted .238 in Nashua in 91 games, as he missed playing time when he fractured his wrist on two occasions. Pirates' manager Chuck Tanner wanted Khalifa to begin the 1985 season as a member of the Pirates' major league roster, but Pete Peterson, the Pirates' general manager, decided that Khalifa needed to spend time in Class AAA before he would be ready for the major leagues. Khalifa started the 1985 season with the Hawaii Islanders of the Class AAA Pacific Coast League, and after batting .282 for the Islanders, he made his MLB debut on June 25, 1985, replacing the injured Johnnie LeMaster, becoming the sixth player to start for the Pirates at shortstop during the 1985 season. The Pirates began the season with Tim Foli and Rafael Belliard. Foli received his release, while Belliard had been demoted to Hawaii. Jerry Dybzinski received one game at shortstop for the Pirates, who was followed by Bill Almon, and the trade acquisition of LeMaster from the Cleveland Indians.