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Bonamigo started his coaching career in 1998 with Madureira, before taking over Joinville in the same year. In 2000 trains Sampaio Corrêa, Remo and Mogi Mirim while in the two following years is at Paraná. In 2002 and 2003 trains Coritiba the mind in 2004, after being coach of Atlético Mineiro, where is Botafogo relieved to mid-season to then be hired by Palmeiras, where it remains up to the rest of the championship in 2005.
In 2009 Bonamigo moved to Al Shabab where he remained until the end of the 2011–12 season, then moved to Al Jazira where he remained until mid-season before being exempted due to the lack of results.