A green and sustainable procedure for obtainingLavandula stoechasextracts with antioxidant and antimicrobial properties was investigated. Green solvents, supercritical CO2, and natural deep eutectic solvents (NADES) together with ultrasound-assisted extraction were used for the sequential extraction of terpene and polyphenols fractions. After the CO2extraction of the terpene fraction, the residue material was used in an extraction with different NADES (betaine-ethylene glycol (Bet:EG), betaine-glycerol (Bet:Gly), and glycerol-glucose (Gly:Glu)), intensified with an ultrasound-assisted method (at 30 and 60 °C). In the CO2extract, the major group of components belonged to oxygenated monoterpenes, while the highest polyphenol content with the dominant rutin (438.93 ± 4.60 µg/mL) was determined in Bet:EG extracts (60 °C). Bet:EG extracts also exhibited the most potent antioxidant activity according to DPPH, ABTS, and FRAP assays. Moreover, Bet:EG extracts showed significant inhibitory activity against Gram-positive and Gram-negative bacteria, with minimum inhibitory activity of 0.781–3.125 and 1.563–6.250 mg·mL−1, respectively. By comparing the polyphenolic content and antioxidant and antimicrobial activities of Bet:EG extracts with extracts obtained with conventional solvents (water and ethanol), the superiority of NADES was determined. The established environmentally friendly procedure unifies the requirements of green and sustainable development and modern pharmacognosy because it combines the use of safe alternative solvents, the absence of solvent waste generation, more rational use of resources, and the attainment of safe and quality extracts.