As opposed to external beam radiation therapy (EBRT), treatment planning systems (TPS) dedicated to intraoperative radiation therapy (IORT) were not subject to radical modifications in the last two decades. However, new treatment regimens such as ultrahigh dose rates and combination with multiple treatment modalities, as well as the prospected availability of dedicated in-room imaging, call for important new features in the next generation of treatment planning systems in IORT. Dosimetric accuracy should be guaranteed by means of advanced dose calculation algorithms, capable of modelling complex scattering phenomena and accounting for the non-tissue equivalent materials used to shape and compensate electron beams. Kilovoltage X-ray based IORT also presents special needs, including the correct description of extremely steep dose gradients and the accurate simulation of applicators. TPSs dedicated to IORT should also allow real-time imaging to be used for treatment adaptation at the time of irradiation. Other features implemented in TPSs should include deformable registration and capability of radiobiological planning, especially if unconventional irradiation schemes are used. Finally, patient safety requires that the multiple features be integrated in a comprehensive system in order to facilitate control of the whole process.