The tough-as-nails defender will head a new eight-person leadership group, with Emily Bates as her deputy.
Koenen served as a vice-captain under Zielke last season and said it is a huge honour to be voted into the top role by her teammates.
"Zilks (Zielke) has created an amazing legacy in her time as captain and I've learnt a lot about what good leadership looks like from her," Koenen said.
"I'm really excited to step up and lead this team as we take on the 2022 season."
Lions coach Craig Starcevich said Koenen is the ideal candidate to take the reins from Zielke.
"Off the field, she's always had great care for her teammates," Starcevich said.
"But it's her selflessness on the field and her understanding of playing her role for the sake of the team that has struck a chord with her teammates.
"Some of the roles she played last year against dangerous opposition has really resonated with her teammates, and it's that combined with the great empathy she's shown that has seen her land in this position."
Zielke hung up her boots after leading Brisbane to their 18-point grand final win over Adelaide in April.
She has since joined Starcevich's coaching panel as an assistant.
Season six of the AFLW competition will begin on January 6.
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