In this study, a model based design methodology for secure IoT nodes is presented. As IoT systems execute various types of tasks, IoT nodes differ according to the requirements. When the requirements related to IoT nodes are analyzed, high security, low power consumption and scalability can be classified as significant requirements. Owing to the fact that these requirements conflicts with each other, a comprehensive design methodology is essentially needed. Model based design methodology which we present in this study aims to address these needs.