Nowadays, almost any IT system involves personal data processing. In such systems, many privacy risks arise when privacy concerns are not properly addressed from the early phases of the system design. The General Data Protection Regulation (GDPR) prescribes the Privacy by Design (PbD) principle. As its core, PbD obliges protecting personal data from the onset of the system development, by effectively integrating appropriate privacy controls into the design. To operationalize the concept of PbD, a set of challenges emerges: First, we need a basis to define privacy concerns. Without such a basis, we are not able to verify whether personal data processing is authorized. Second, we need to identify where precisely in a system, the controls have to be applied. This calls for system analysis concerning privacy concerns. Third, with a view to selecting and integrating appropriate controls, based on the results of system analysis, a mechanism to identify the privacy risks is required. Mitigating privacy risks is at the core of the PbD principle. Fourth, choosing and integrating appropriate controls into a system are complex tasks that besides risks, have to consider potential interrelations among privacy controls and the costs of the controls. This thesis introduces a model-based privacy by design methodology to handle the above challenges. Our methodology relies on a precise definition of privacy concerns and comprises three sub-methodologies: model-based privacy analysis, modelbased privacy impact assessment and privacy-enhanced system design modeling. First, we introduce a definition of privacy preferences, which provides a basis to specify privacy concerns and to verify whether personal data processing is authorized. Second, we present a model-based methodology to analyze a system model. The results of this analysis denote a set of privacy design violations. Third, taking into account the results of privacy analysis, we introduce a model-based privacy impact assessment methodology to identify concrete privacy risks in a system model. Fourth, concerning the risks, and taking into account the interrelations and the costs of the controls, we propose a methodology to select appropriate controls and integrate them into a system design. Using various practical case studies, we evaluate our concepts, showing a promising outlook on the applicability of our methodology in real-world settings.