Cerebra-QSM is a modular C++ application for quantitative susceptibility mapping that logs the inputs and results from each stage of the QSM processing pipeline. It provides a user interface for analysis, review and process validation, as well as a scripting interface for batch processing. It is flexible and intuitive, allowing rapid evaluation of algorithms and training of end-users on the specifics of QSM estimates. It has been adopted by multiple researchers, facilitating independent work. Cerebra-QSM provides a robust, simple and scalable framework for evaluation of processing pipelines.