Khalifa recorded six hits in his first eleven at-bats. In his rookie season, he had a .238 batting average across 95 games played. In 1986, Khalifa platooned at shortstop with Rafael Belliard, as Khalifa struggled, batting .185. He was sent down to the minor leagues, and Jay Bell solidified himself as the Pirates' starting shortstop. Khalifa played for the Vancouver Canadiens of the Pacific Coast League in 1987. He split the 1988 season with the Harrisburg Senators of the Eastern League and the Buffalo Bisons of the Class AAA International League. He again played for Buffalo in 1989. One day, he was five minutes late for the team bus, it left without him, and he returned home to Tucson.