Targets have been agreed to restore 20 per cent of damaged land areas and 20 per cent of seas by 2030 and have policies in place for all ecosystems by 2050.
But horse-trading in Brussels led to the package being watered down as conservatives won concessions on policies affecting farmland.
The package now ready for a vote is "essential to reach the EU’s ambitious climate mitigation and adaptation goals", said Maros Sefcovic, the commissioner overseeing the bloc's Green Deal plans.
"This also sends an important positive signal to our global partners ahead of Cop28," he said. "There’s no time to lose in restoring nature that our wellbeing and economies depend on."
Included in the deal are measures to protect biodiversity such as birds and butterflies, restore habitats in rivers and forests and ensure there is no loss of trees and green spaces in cities.
Member states would also commit to taking action to reverse the declining population of pollinators, such as bees, and submit an overall nature restoration plan within two years.
The centre-right European People's Party celebrated blocking a proposal to return 10 per cent of farmland to nature, which it said would have pushed up food prices.
Measures affecting agriculture can also be suspended if there is a food security crisis, an "emergency brake" that Greens in the European Parliament had opposed. The revised package will now need formal approval from the parliament and the council representing the EU's 27 members.
The European Commission's original proposal was "ideologically driven, practically unfeasible and a disaster for farmers", said EPP negotiator Christine Schneider. "We are glad to see that the other political groups have moved in our direction."