The US company said the two sides had struck a “definitive agreement” worth at least US$85m.
Under the deal, Atlanta will still act as Chiquita’s distributor in Germany and Austria.
Chiquita chairman and CEO Fernando Aguirre said the deal was “yet another important step in the execution of our profitable growth strategy”.
He added: “This transaction will enable us to increase our focus on providing branded, healthy, fresh foods to consumers worldwide, while ensuring that we continue to provide reliable, high-quality ripening and distribution of Chiquita bananas in the German and Austrian markets.”
The EU will now look at the deal, which is expected to be completed over the summer.