Nowadays, plant-based bioactive compounds (BCs) are a key focus of research, supporting sustainable food production and favored by consumers for their perceived safety and health advantages over synthetic options. Lavandula pedunculata (LP) is a Portuguese, native species relevant to the bioeconomy that can be useful as a source of natural BCs, mainly phenolic compounds. This study compared LP polyphenol-rich extracts from conventional maceration extraction (CE), microwave and ultrasound-assisted extraction (MAE and UAE). As a result, rosmarinic acid (58.68–48.27 mg/g DE) and salvianolic acid B (43.19–40.09 mg/g DE) were the most representative phenolic compounds in the LP extracts. The three methods exhibited high antioxidant activity, highlighting the ORAC (1306.0 to 1765.5 mg Trolox equivalents (TE)/g DE) results. In addition, the extracts obtained with MAE and CE showed outstanding growth inhibition for B. cereus, S. aureus, E. coli, S. enterica and P. aeruginosa (>50%, at 10 mg/mL). The MAE extract showed the lowest IC50 (0.98 mg DE/mL) for angiotensin-converting enzyme inhibition and the best results for α-glucosidase and tyrosinase inhibition (at 5 mg/mL, the inhibition was 87 and 73%, respectively). The LP polyphenol-rich extracts were also safe on caco-2 intestinal cells, and no mutagenicity was detected. The UAE had lower efficiency in obtaining LP polyphenol-rich extracts. MAE equaled CE’s efficiency, saving time and energy. LP shows potential as a sustainable raw material, allowing diverse extraction methods to safely develop health-promoting food and nutraceutical ingredients.