A method and system for normalizing an IMPT plan are provided as well as an arrangement for planning IMPT and a computer program product comprising instructions to perform the method. The method comprises the steps of: receiving an IMPT plan for a subject to be treated, receiving anatomical image data of the subject comprising at least one ROI, and receiving at least one clinical goal associated with the ROI. The method further comprises identifying one or more deficiency areas of the IMPT plan within the ROI where the clinical goal is not met, and identifying the particle spots of the IMPT plan that are associated with the identified deficiency areas as critical particle spots. When the critical spots have been identified, the method comprises normalizing at least one of the deficiency areas by adjusting the intensity of the critical particle spots.