Recognition of per- and polyfluoroalkyl substances (PFAS) as widespread environmental pollutants and a consequent risk to human health, has recently made the European Union (EU) adopt several regulatory measures for their management. The coherence of these measures is challenged by the diversity and the ubiquitous occurrence of PFAS, which also complicates the EU’s endeavor to advance justified, harmonized, and transparent approaches in the regulatory assessment of chemical risks. Our study critically reviews the European approach for the risk assessment of PFAS, by applying a comparative analysis of the current and pending regulatory thresholds issued for these chemicals in water bodies, drinking water, and certain foodstuffs. Our study shows that the level of health protection embedded in the studied thresholds may differ by three orders of magnitude, even in similar exposure settings. This is likely to confuse the common understanding of the toxicity and health risks of PFAS and undermine reasonable decision-making and the equal treatment of different stakeholders. We also indicate that currently, no consensus exists on the appropriate level of required health protection regarding PFAS and that the recently adopted tolerable intake value in the EU is too cautious. Based on our analysis, we propose some simple solutions on how the studied regulations and their implicit PFAS thresholds or their application could be improved. We further conclude that instead of setting EU-wide PFAS thresholds for all the environmental compartments, providing the member states with the flexibility to consider case-specific factors, such as regional background concentrations or food consumption rates, in their national regulatory procedures would likely result in more sustainable management of environmental PFAS without compromising the scientific foundation of risk assessment, the legitimacy of the EU policy framework and public health.