The selection of the best-fit-for-purpose analytical method to be implemented in the laboratory is difficult due to availability of multiple methods, targets, aims of detection, and different kinds and sources of more or less reliable information. Several factors, such as method performance, practicability, cost of setup, and running costs need to be considered together with personnel training when selecting the most appropriate method. The aim of our work was to prepare a flexible multicriteria decision analysis model suitable for evaluation and comparison of analytical methods used for the purpose of detecting and/or quantifying genetically modified organisms, and to use this model to evaluate a variety of changing analytical methods. Our study included selection of PCR-, isothermal-, protein-, microarray-, and next-generation sequencing-based methods in simplex and/or multiplex formats. We show that the overall result of their fitness for purpose is relatively similar; however, individual criteria or a group of related criteria exposed more substantial differences between the methods. The proposed model of this decision support system enables easy modifications and is thus suitable for any other application of complex analytical methods.