Kubiak reentered baseball as a manager and took over as the manager of the Modesto A's in mid-1989 from Lenn Sakata. He remained in Modesto for four more years before joining the Cleveland Indians organization in 1994. He managed the Canton–Akron Indians in 1994 and 1995, then moved down to the New York–Penn League for five years. He was with the Watertown Indians from 1996 to 1998, and the Mahoning Valley Scrappers in 1999 and 2000. He moved up to the Columbus RedStixx in 2001, the Kinston Indians in 2002, then returned to Mahoning Valley in 2003. From 2004 to 2008 he was the minor league defensive coordinator for the Cleveland Indians. In 2009, he returned to managing with the Arizona Extended League Indians, in 2010 managed the Lake County Captains to the Midwest League Championship, and in 2012 he returned to Mahoning Valley to begin his 4th season at the helm of the Scrappers.
