The Dockers confirmed on Monday night they would not renew Cooper's contract after he failed to make playoffs for the first time in five seasons.
Fremantle missed out on the top eight, finishing 12th after only managing three wins and a draw in a season smashed by injuries.
Ebony and Kara Antonio missed most of the season, captain Hayley Miller had a limited pre-season and superstar on-baller Kiara Bowers took time to hit her straps.
"It's been a challenging period for our AFLW program, this is something we acknowledged when we sat down with Trent as part of the review process into our AFLW season seven," chief executive Simon Garlick said in a video on Fremantle's website.
"It became apparent that we were looking for a reset and refresh in our approach.
"These are always difficult decisions when they relate to great football people.
"... this decision isn't so much related to performances of the past but of what we need moving into the future."
Garlick said the Dockers believed their squad could bounce back quickly and return to premiership contention.
Cooper took over from inaugural coach Michelle Cowan after the 2018 season.
He quickly had an impact, taking Fremantle to their first finals appearance in 2019.
"I have met some special people over my time here and I'm extremely proud of what we have been able to achieve together," Cooper said in a statement.
"This is a tough moment for me because I work with an incredible group of people.
"I'm grateful for the support I've had along the way, whether that be from the club, fans, our sponsors, the staff, my coaches, my players or my family, and it's something I will always cherish."
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