In this paper, we present a method for patching embedded multitasking real-time systems applications during runtime, for instrumentation purposes. The method uses binary modification techniques and automates the entire patch process. The method makes it possible to insert and remove instrumentation code without preparing the original source code. The method makes it possible to invoke code patches during run-time, without having to rely on dynamic linking of object files, or predeployment prepared dormant code. The actual modification of the executing target binary is performed in a safe and controlled manner by a dedicated low interference mutation task.