Following the departure of Mark Miller, Balzan FC came to an agreement on a two-year deal with Paul Zammit to take over the coaching of their Premier League squad.

Club President Anton Tagliaferro said: “We look forward to Paul joining the club and guiding the team to help the club reach its objectives for this season and beyond.”

At the end of 2003, Paul Zammit retired as a player and started his coaching career with Mosta FC.

In 2005, he moved to Valletta FC and in 2008, he won the Maltese Coach of the Season award for coaching Valletta to victory in the Maltese Premier League. In September 2008 he signed another two-year contract to continue coaching Valletta FC.

In the 2009/10 season, Paul Zammit became the head coach of Birkirkara FC and in April 2010, he won the Maltese Premier League title. At the end of season 2010–11 season, Zammit was re-appointed as the club’s head coach up to season 2014/2015.

In 2015 he took over the Valletta FC team once again and coached them for two seasons.

In 2017 he rejoined Birkirkara FC however, he was forced to leave in January 2019 because of the appointment of John Arne Riise as Sporting Director.

In January 2020 he had a spell as the Head Coach of Gzira U FC, as he stepped down at the end of the season.