This study represents the first work integrating theory and practice from the field of fact-checking and combating fake news into a novel methodology for performance analysis of fact-checking organizations. It provides important insights into the efficiency and effectiveness of European fact-checking organizations. However, it is relevant for any fact-checking organization across the Globe. The methodology includes the development of a scheme of performance indicators and the definition of a taxonomy of fact-checking systems, supported by an existing conceptual framework. The practical part consists of piloting of the methodology into a set of implemented and working online platforms. The results from the study reveal huge space for improvements of the workflows and the functionality of fact-checkers and lead to the extraction of a set of recommendations in this regard.