Utilising insights from policy instrument theory, the article analyses the design, functioning and effects of the tools used by the Czech Accreditation Commission (CAC) and the Slovak Accreditation Commission (SAC) in the 2000s. Aside from programme accreditation, the other tools analysed are: institutional approval, institutional evaluations, evaluations of accredited activities and complex accreditations. Czech and Slovak programme accreditation is empirically evidenced to be very burdensome and have limited effectiveness. The commissions' evaluative activities reveal some inconsistency of recommendations and missing follow-ups. Overall, the analysis suggests that the spillover effects of on-site evaluations on accreditation verdicts are likely to limit long-term improvement intra-institutionally, causing inconsistency of the instrument mix applied by the CAC and the SAC. Due to these design discrepancies, the change-over from programme accreditation to quality audit, resulting in an approval-audit mix, is argued for as a viable development trajectory of Czech and Slovak systemic quality assurance.