Currently, treatment planning for intensity modulated proton therapy (IMPT) usually disregards variations of the relative biological effectiveness (RBE). To investigate the potential clinical relevance of a variable RBE for beam scanning techniques, new strategies for the evaluation of radiobiological effects and for the incorporation of the RBE into the inverse planning process are presented. These strategies are based on a fast algorithm for three‐dimensional calculations of the dose averaged linear energy transfer (LET) as a measure of the local radiation quality, and on a simple phenomenological approach for the RBE as a function of dose, LET and tissue type. It was found that the biological effect depended strongly on the type of scanning technique used, mainly due to differences in the LET distributions. New objective functions that account for LET and RBE were integrated into an inverse planning software, which now allows simultaneous multifield optimization of the biological effect in a reasonable time. With these methods, unfavorable RBE effects can be identified and compensated for by direct optimization of the product of RBE and dose, which is demonstrated for several clinical examples. The proposed strategies are therefore valuable tools to evaluate and improve the quality of treatment plans in IMPT.