External radiotherapy with proton and ion beams needs accurate tools for the dosimetric characterization of treatment fields. Monte Carlo (MC) particle transport codes, such as FLUKA and GEANT4, can be a valuable method to increase accuracy of dose calculations and to support various aspects of ion beam therapy (IBT), such as treatment planning and monitoring. One of the prerequisites for such applications is however that the MC codes are able to model reliably and accurately the relevant physics processes. As a first focus of this thesis work, physics models of MC codes with importance for IBT are developed and validated with experimental data. As a result suitable models and code configurations for applications in IBT are established. The accuracy of FLUKA and GEANT4 in describing nuclear fragmentation processes and the production of secondary charged nuclear fragments is investigated for carbon ion therapy. As a complementary approach to evaluate the capability of FLUKA to describe the characteristics of mixed radiation fields created by ion beams, simulated microdosimetric quantities are compared with experimental data. The correct description of microdosimetric quantities is also important when they are used to predict values of relative biological effectiveness (RBE). Furthermore, two models describing Compton scattering and the acollinearity of two-quanta positron annihilation at rest in media were developed, validated and integrated in FLUKA. The detailed description of these processes is important for an accurate simulation of positron emission tomography (PET) and prompt-γ imaging. Both techniques are candidates to be used in clinical routine to monitor dose administration during cancer treatments with IBT. The second objective of this thesis is to contribute to the development of a MC-based treatment planning tool for protons and ions with atomic number Z ≤ 8 using FLUKA. In contrast to previous clinical FLUKA-based MC implementations for IBT which only re-calculate a given treatment plan, the developed prototype features inverse optimization of absorbed dose and RBE-weighted dose for single fields and simultaneous multiple-field optimization for realistic treatment conditions. In a study using this newly-developed tool, the robustness of IBT treatment fields to uncertainties in the prediction of RBE values is investigated, while comparing different optimization strategies.