Engineering tools support the process of creating, operating, maintaining, and evolving systems throughout their lifecycle. Toolchains are sequences of tools that build on each others' output during this procedure. The complete chain of tools itself may not even be recognized by the humans who utilize them, people may just recognize the right tool being used at the right place in time. Modern engineering processes, however, do not value such ad-hoc choice of tooling, because of their uncontrolled nature. Building upon the Extended Automation Engineering Model defined by the IEC 81346 standard, this paper proposes to automate the toolchain building and execution process for Cyber-Physical System of Systems (CPSoS), utilizing key principles of the Eclipse Arrowhead framework. The proposed toolchain automation solution addresses issues such as tool interoperability, interaction, automation, and dynamic choreography. The feasibility of this set of integrated concepts is validated through an Arrowhead-based toolchain choreography demonstration.Note to Practitioners-The paper discusses approaches to the automated execution of various industry-related processes. As the processes are becoming more complex and involve numerous systems which have to be orchestrated, a simple and preprogrammed workflow is not enough anymore. Therefore, building on top of the principles of the Eclipse Arrowhead framework, an adequate model of toolchains, allowing for their automated execution, is proposed. Different approaches to supervision of toolchain execution are discussed showing the benefits of reaching higher automation levels. Further, four adoption levels are introduced, which are a measure of the toolchain automation progress. Finally, a simplified demonstrator is shown and steps to elevate it to higher adoption levels are highlighted. To ensure that the approach is industry-oriented, several examples of how the proposed methodology can be used in the industrial context are discussed.