In the Directorate of Operations, the control activities of the FOCBS are managed. With around 3,500 employees, it ensures security and border monitoring. The strategic leadership is centralized, while the operational management is organized across six regional levels, which are structured as follows:
- Customs North: Basel Stadt, Basel Landschaft, Aargau
- Customs Northeast: Schaffhausen, Thurgau, Zurich, Zug, Schwyz, Lucerne, Obwalden, Nidwalden, Glarus
- Customs East: St Gallen, Appenzell Innerrhoden, Appenzell Ausserrhoden, Graubünden, Principality of Liechtenstein
- Customs South: Uri, Ticino
- Customs West: Geneva, Vaud, Valais
- Customs Central Switzerland: Jura, Neuchâtel, Bern, Fribourg, Solothurn
