Flanagan was named vice president of baseball operations Wednesday and will report to Beattie, who was named by owner Peter Angelos as executive vice president of baseball operations.
They would serve as the replacements for vice president of baseball operations Syd Thrift, who has been the Orioles' de facto general manager over the last three seasons. The 73-year-old Thrift said after the season that he did not expect to return in the same role in 2003.
The Orioles were fourth in the American League East last season with a 67-95 record and their farm system is considered among the worst in baseball.
Flanagan, 50, was the 1979 American League Cy Young Award winner with the Orioles, but has no previous front office experience. He has been around the Orioles organization for more than two decades as a player, pitching coach, broadcaster and advisor to Angelos.
Beattie, 48, brings considerable front office experience as general manager of the Montreal Expos for six seasons. Working with a limited budget, Beattie was often able to field young, competitive teams. He pitched for the New York Yankees and Seattle Mariners in the late 1970s and early 1980s.
Beattie, a native of nearby Hampton, Virginia, resigned as general manager of the Expos after the 2001 season when Major League Baseball took control of the team.
Former Orioles superstar Cal Ripken publicly stated his desire to run the team last month, but later pulled himself out of the running before officially interviewing.
The Orioles are the last team in the major leagues to fill the role of general manager after the Boston Red Sox named Theo Epstein last week.