Microprocessor-based embedded systems are increasingly used to control safety-critical systems (e.g., air and railway traffic control, nuclear plant control, aircraft and car control). In this case, fault tolerance mechanisms are introduced at the hardware and software level. Debugging and verifying the correct design and implementation of these mechanisms ask for effective environments, and Fault Injection represents a viable solution for their implementation. In this paper we present a Fault Injection environment, named FlexFI, suitable to assess the correctness of the design and implementation of the hardware and software mechanisms existing in embedded microprocessor-based systems, and to compute the fault coverage they provide. The paper describes and analyzes different solutions for implementing the most critical modules, which differ in terms of cost, speed, and intrusiveness in the original system behavior.