In this paper, the theoretical perspectives and general methodological elements of impact evaluation of quality assurance in higher education institutions are discussed, which should be a cornerstone of quality development in higher education and contribute to improving the knowledge about the effectiveness (or ineffectiveness) of quality assurance. The suggested core methodology consists in comparative and longitudinal studies carried out simultaneously to the quality assurance interventions and relying on surveys and mixed methods. The methodology is applicable to any particular quality assurance procedure and any achievement area of higher education institutions. To round off the methodology presentation, an overview of causal designs, in particular causal social mechanisms, for impact analyses of quality assurance in higher education institutions and its challenges and limits is outlined and some characteristics of survey questionnaire construction are given.