The European Union lacks comprehensive legislation pertaining to food supplements containing botanical or bioactive substances other than nutrients, resulting in disparate regulatory frameworks among European Member States. Previous studies predominantly focused on the doctrinal analysis of these diverse regulations at both European and national levels, offering limited insights into their practical implementation by governing bodies. This research endeavours to scrutinize administrative practices governing legislation on food supplements featuring botanical or other bioactive constituents, which are subject to varying approaches across Member States. Employing a combination of doctrinal and empirical legal research methodologies, this approach involved a meticulous examination of the regulatory landscape governing food supplements at both EU and Member State levels. Simultaneously, an empirical investigation, conducted through expert interviews, aimed to elucidate whether discrepancies among national legal systems translate into discernible variations in the operational strategies of competent authorities. Additionally, this empirical inquiry shed light on the efficacy of specific EU directives aimed at harmonizing food supplement regulations at the national level. These findings delineate a fragmented regulatory environment for botanical and bioactive food supplements across Member States. Noteworthy disparities were observed not only in national legislative frameworks but also in the enforcement practices of regulatory authorities. Union-level governance efforts in particular by adopting a mutual recognition approach to mitigate fragmentation proved ineffective. Consequently, this research underscores an urgent imperative to expedite the harmonization of regulations governing botanicals and other bioactive substances present in food supplements across the European Union.