A method of operating a multi-beam particle beam system includes: generating a multiplicity of particle beams such that they each pass through multipole elements that are either intact or defective; focusing the particle beams in a predetermined plane; determining excitations for the deflection elements of the multipole elements; exciting the deflection elements of the multipole elements that are intact with the determined excitations; modifying the determined excitations for the deflection elements of the multipole elements that are defective; and exciting the deflection elements of the defective multipole elements with the modified excitations. Modifying the determined excitations includes adding corrective excitations to the determined excitations. The corrective excitations are the same for all deflection elements of the defective multipole element.