He started his managerial career at Naval in 2003. In 2008 he made a brilliant job with [F.C. Tirsense|Tirsense] putting the team in Portuguese Premier League. In 2009, he took control of Liga 1 team CFR Cluj where he won everything that season, becoming Champion of the Romanian Premier League and Champion of the Romanian Cup and Champion of the Romanian Supercup. In the next season he accepted the invitation to back to Portugal and signed for Belenenses to replace Joao Pereira.
One year after he came back to Romania, where he managed FC Braşov for one season. In January 2012, he signed a contract with Astra Ploiești,.
Toni returned to Portugal in October 2012 to manage Braga leaving the club after the end of the season to coach Moreirense F.C.. Once again he could make a great job, winning the Portuguese 2nd League and putting Moreirense in Portuguese Premier League. At the end of the season he was invited do renew his contract with Moreirense but he didn't accepted the conditions offered by the club and quit, preferring to wait for a new project.