Abstract Petasites hybridus extracts are valued for their antimigraine and anti-inflammatory properties but require pyrrolizidine alkaloids-free and compositionally consistent extraction methods. Supercritical CO₂ extraction offers an alternative to organic solvents, yet its performance for butterbur has not been systematically optimized or linked to chemical and biological outcomes. This study aimed to optimize extraction conditions using Box–Behnken design and evaluate extraction yield, sesquiterpenoid content, pyrrolizidine alkaloids levels, and cyclooxygenase-2 (COX-2) inhibitory activity across the investigated extraction conditions. Fifteen extracts were prepared across a three-factor Design of Experiments (DOE). Sesquiterpenoids and pyrrolizidine alkaloids were quantified using UPLC-PDA-MS/MS. COX-2 inhibition was assessed using a fluorometric screening assay. Data were modelled using response surface methodology and multivariate regression analysis. Extraction yield responded to temperature and CO₂ consumption, while sesquiterpenoid composition remained stable. Supercritical CO₂ extraction with the dried plant material yielded pyrrolizidine alkaloids-poor extracts (15–91 µg/g), whereas PAs content increased > 100-fold after hydrating the same plant material to a 40% moisture content and continuing the process. COX-2 inhibition was moderate (49–65% relative to the positive control, Celecoxib), reproducible, and insensitive to extraction parameters or individual metabolite levels. Overall, supercritical CO₂ extraction provides a scalable method for producing compositionally stable P. hybridus extracts with low pyrrolizidine alkaloids content. While extraction yield can be efficiently optimized, the biological activity appeared to be matrix-driven. Future enhancement of anti-inflammatory potency will require fractionation or co-solvent strategies rather than modifications of operating supercritical CO₂ extraction conditions.