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Jacobs said the time was right for him to move on after 13 years at the club - the last three of which was spent as CEO - with head coach Tony Popovic arriving in July on a three-year deal with a licence to effectively overhaul the Victory.
"With a refresh of our football department due to occur when Tony Popovic takes the helm for next season, now is the right time to depart the club as it heads towards a new era both on and off the pitch," Jacobs said.
"It has been a very difficult 14 months, in particular through COVID-19, and after reflecting over the past few weeks I made the difficult decision not to continue in the chief executive role.