An ATR certificate is a Customs document that can be used bij trade between EU countries and Turkey. The EU has an Customs agreement with Turkey that says that most goods can be imported without duties. Goods need to come from the EU or Turkey. This will be stated in a ATR certificate.
The ATR certificate can not be used for most agrical products and steel products. For these products the origin is significant and need a EUR-1 certficate. Customs has a complete list of the excluded products. Your Chamber of Commerce (Department Export Products) will inform you which document will aplly for your goods.
In case of export to Turkey, the ATR certificate needs to be filled in by the exporter. Customs makes the valid export license. This happens simultaneously with the export declaration.
If the certificate is used to import goods from Turkey, you need to deliver an ATR certificate together with the import declaration to the customs. This certificate is validated by the Turkish customs. (source: Dutch Chamber of Commerce)