Addressing the World Economic Forum by videolink, von der Leyen said the EU would lobby for such a deal at the COP-15 UN biodiversity summit in Kunming, China expected to take place later this year.
"This will have to be like COP21 was for climate, because we need a Paris-style agreement for biodiversity," she said.
The Kunming summit was postponed last year due to the coronavirus epidemic, and world governments are focused on fighting the outbreak and restarting their economies.
But von der Leyen, herself a trained doctor before becoming a German politician, said protecting a diverse range of species and habitats could be key to protecting human health.
"If we don't urgently act to protect our nature, the next pandemic will be around the corner," she said, citing an anecdote that suggested deforestation in Africa had displaced bats and contributed to an Ebola outbreak.
"To those who prefer the business case, here it is: More than half of global GDP is dependent on high-functioning biodiversity and ecosystem services -- from food to tourism," she said.
The World Economic Forum is an annual get-together of political and business leaders, traditionally held in the Swiss resort of Davos, but this year held online.
Von der Leyen hailed new US President Joe Biden's early decision to return to the 2016 Paris Climate Agreement, which his predecessor Donald Trump had abandoned.
And she said that the European Commission's economic recovery plan -- her so-called Green Deal -- would boost growth while reducing greenhouse emissions and protecting biodiversity.
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