Embedded systems show the tendency of becoming more and more connected. This fact combined with the trend towards the Internet of Things, from which measuring instruments are not immune (e.g., smart meters), lets one assume that security in measuring instruments will inevitably play an important role soon. Additionally, measuring instruments have adopted general-purpose operating systems to offer the user a broader functionality that is not necessarily restricted towards measurement alone. In this paper, a flexible software system architecture is presented that addresses these challenges within the framework of essential requirements laid down in the Measuring Instruments Directive of the European Union. This system architecture tries to eliminate the risks general-purpose operating systems have by wrapping them, together with dedicated applications, in secure sandboxes, while supervising the communication between the essential parts and the outside world.