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In recent years, biometrics is being used more and more in security applications. This fact has led suppliers and researchers to analyze biometric algorithms powers and vulnerabilities, as to improve the feasibility of this technology. Nevertheless, as many authors claim, biometric performance also depends on other factors such as usability and/or user acceptance, which can influence significantly their performance. Only a few of these factors have already been studied, using specific approaches and only for certain biometric modalities, such us fingerprint and face. However, there is no general and independent methodology implemented to assess how these factors affect biometric system performance and to produce intercomparable results. Based on previous works and following procedures and requirements addressed in the International Standard ISO/IEC 19795-2 for scenario evaluations, these authors have developed a general methodology to analyze end-to-end system performance when some usability factors are modified. Such factors cover different ways of presenting biometric characteristics to the sensor and also the biometric characteristic variability caused by illness or climatic changes. A generic and controlled scenario has been modelled to carry on all sets of trials. Then, the methodology has been particularized defining specific protocols, methods, and considerations for each parameter to assess. Furthermore, details for analysing these parameters through different modalities have been defined. In addition, this methodology has been checked for one modality considering different usability aspects to obtain the feedback necessary to test its validity and viability and to detect points of interest for improvement. Results, main conclusions, and suggestions for test operators will be presented.