The COVID-19 pandemic forced national governments and administrations to seek flexible solutions to deal with the emergency. Thus, the main purpose of the current study is to design a model of a flexible methodology based on detailed flexible methodologies to make decisions and measures connected to COVID-19 pandemic to be effectively applied without the loss of meaning and within a short time. For the creation of the methodology, we used comprehensive desk research based upon a literature review in the period May 2021–November 2021. As a result, an expandable set of relevant methodologies for crisis management and flexible methodologies was identified, modeled, and formalized using a broad literature review and an innovative model of a flexible methodology for crisis management was created in accordance with standardized concepts, transforming them into secondary use models. Furthermore, an algorithm for taking measures and decisions in crisis conditions was designed. The next step is to implement the methodology, which is planned for future empirical research. The findings provide an innovative model of a flexible methodology that could be used by academic and business representatives, public institutions of central and local government, and private stakeholders.