Ponfoort, who joined the expedition cruise company in 2020, will stay on with the business to assist it through a transitional period.
During her time with Aurora, she launched the brand’s Sustainability In Action programme and led the business’s global growth in key source markets and development of industry partnerships with Virtuoso and Qantas.
Ponfoort said she was confident the company is "well positioned" to continue its growth.
"I have achieved the goals I had set out for Aurora Expeditions when I joined the business in 2020," she added.
"Personally, I am excited and ready for a new challenge, and I wish the Aurora team every success for the future."
Aurora Expeditions chairman Neville Buch said: "We wish to personally thank Monique for her valued contribution and leadership of Aurora Expeditions during this difficult time and getting us back to what we do best."