Mooney coached the Coyote baseball team from 1987-2000, compiling a 526-239-3 all-time record, including 14-consecutive postseason appearances. He led the Yotes to three-consecutive NAIA World Series appearances, winning the 1998 National Championship, placing second in 1999, and fifth in 2000. Mooney, who coached 23 NAIA All-Americans, was named NAIA Coach of the Year in 1998 and was Cascade Conference Coach of the Year on five occasions.