Embedded devices are crucial enablers of the Internet of Things and become increasingly common in our daily life. They store, manipulate and transmit sensitive information and, therefore, must be protected against security threats. Due to the security and also resource constraint concerns, designing secure networked embedded systems is a difficult task. Model-based development (MBD) is promoted to address complexity and ease the design of software intensive systems. We leverage MBD and domain-specific modelling to characterise common issues related to security and embedded systems that are specific to a given application domain. Security-specific knowledge relevant for a certain application domain is represented in the form of an adapted information security ontology. Further, the elements of the ontology are associated with security building blocks modelled with the MBD method SPACE. The selection of relevant security building blocks is based on (i) assets automatically elicited from the functional models, (ii) domain security knowledge captured by the security expert and (iii) the platform adopted by the embedded system engineer. A tool is developed to support the steps supporting this methodology and help to bridge between the security and embedded systems domains. We illustrate our approach with a case study from the smart metering domain. © 2013 The Authors. Security and Communication Networks published by John Wiley & Sons, Ltd.