Trade barriers will be lifted Aug. 1 following Colombia's ratification in June of the trade agreement that includes Peru, the commission said.
It is expected the trade deal will reduce tariff costs to companies by $663 million annually. But the agreement is also intended to increase trade, which would mean increased revenue for exporters.
"The main benefit of the new trade regime will come from a more transparent, predictable and enforceable business environment," the European Commission said in a statement.
The new trade agreement has already been implemented by the eurozone and Peru, as Peru ratified the agreement in time to put it into effect in the spring.
The three parties signed the deal in June 2012.
With the trade deal in place, there will be no duties on industrial and fisheries products and agricultural trade will be "considerably more open," the commission said.
In addition, the agreement calls for human rights, labor laws and environmental protections that are on par with "international conventions," the commission said.