The Joint Assessment Team and the Battalion fall under the strategic command of the Supreme Allied Commander Europe (SACEUR). Operational control is delegated to a subordinate command as required.

Allied Command Transformation (ACT) provides evaluation standards, supports training and determines future CBRN defence requirements and develops capabilities.

The battalion-level structure is composed of personnel from a number of NATO countries, on stand-by for 12-month rotations. It may also include personnel and CBRN defence assets from partner countries. Similar to the NATO Response Force (NRF), dedicated personnel are based in their countries, coming together for training and deployment.