Nefyto consists of a general board, in which all the member companies are represented, and an executive board which is responsible for the day-to-day running of the organization and for external affairs. As of 1 April 2010 the executive board consists of:

Nefyto's advisers on legal and policy matters are Brabers in The Hague, at whose offices the secretariat is also situated. Brabers undertake a great deal of non-secretarial work for Nefyto as well and are also Nefyto's point of contact for internal and external relations. Nefyto matters are handled by Maritza van Assen (director), Jo Ottenheim (secretary) and Armida Velghert (executive secretary).
In addition, the following permanent working groups are active:
- The Agriculture Working Group deals with the approval of crop protection products and agricultural aspects of the use of such products.
- The Core Team consists of senior specialists, each co-ordinating one or more groups of specialists in the field of environment, water, worker safety, food safety and agriculture.
- The Distribution Working Group co-ordinates matters of logistics (such as labelling and storage).
- The Communications Working Group is responsible for Nefyto's policy on communications.