The city said Thursday that it had obtained the necessary easements to begin construction.
The company has promised to create about 1,000 new jobs in its planned move to the South Bronx.
The board voted by a wide margin to back a lease modification the company needs to move to The Bronx.
A group of residents filed a lawsuit trying to block the company from building a new base in The Bronx.
Urban planners suggested parks and community spaces would be a better use of the South Bronx waterfront.
FreshDirect, whose headquarters was in an evacuation zone, lost dozens of trucks in the storm.
The online grocer hired the award-winning eco-activist as a consultant to engage local groups.
Stalled plans for a pedestrian bridge to connect Port Morris and Randall's Island are moving forward.
Critics had slammed Fresh Direct for taking public subsidies, but only delivering to the north Bronx.
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