The new rules enter into force today (1 July), making the 'Euro-Leaf' label mandatory on pre-packaged organic foods that meet organic farming standards.
The logo stays optional for non-packed and imported organic products and other private, regional or national logos can still be displayed next to the EU label.
In addition to the logo, the new rules also require operators to indicate where a product's ingredients were farmed and give the code number of the body that performed the checks.
"I hope that these changes will give a boost to the organic farming sector, but also further enhance consumer protection," said EU Agriculture Commissioner Dacian Cioloş.
Operators have a two-year transition period to comply with the new rules.
Another change that comes into effect today is the introduction of the first-ever EU rules setting conditions for organic aquaculture.
They require the separation of organic and non-organic units and specify animal welfare conditions, including maximum stocking densities.
The rules also prohibit the use of induced spawning by artificial hormones and require the use of organic feeds which may be supplemented by fish feeds derived from sustainably managed fisheries.
The new organic labelling rules will also cover organic aquaculture production of fish, shellfish and seaweed.
Fisheries Commissioner Maria Damanaki stressed that the new EU rules for organic aquaculture are "a boost for sound and environmentally-acceptable production and a viable alternative to the more traditional intensive approach," predicting that they will give consumers more choice.