In this paper, we report the effect of skullcap (Scutellaria baicalensis Georgi) root (SR) and buckwheat (Fagopyrum esculentum Moench) husk and stalk (BH and BS) extracts on lipid organization and fluidity of model membranes, examined by monitoring of the thermotropic phase transition of dimyristoylphosphatidylcholine (DMPC) with differential scanning calorimetry, attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) and fluorescence spectroscopy. Despite the very high biological activity of these extracts, such a study has not been undertaken previously. Calorimetric results on the thermotropic parameters of DMPC membranes suggest that BH and BS extracts modify them to a greater extent than SR. Fluorescence and ATR-FTIR results confirm that the compounds contained in the SR extract concentrate in the hydrophilic area of the DMPC bilayer, causing an increase in the order of the polar heads of the lipid, and they do not penetrate the hydrophobic area. Compounds contained in the BS and BH extracts also concentrate in the hydrophilic area of the bilayer; however, they partially affect the hydrophobic-hydrophilic interface of the bilayer as well as the upper part of the acyl chain region.