Catechin flavonoids are the main components of green tea extracts which present broad potential physiological activities. Several of their biological activities seem to affect membrane-dependent cellular processes and it is known that some catechins interact with phospholipid membranes. In this study we examine the interactions of a 3-O-(3,4,5-trimethoxybenzoyl)-(-)-catechin (TMCG), and its quinone methide (QM) activated product with 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) membranes by means of differential scanning calorimetry, X-ray diffraction, Fourier-Transform infrared spectroscopy and molecular dynamics simulation. We report that there are extensive interactions between TMCG and DPPC involving the perturbation of the thermotropic gel to liquid crystalline phase transition of the phospholipid, the decrease of bilayer thickness and the promotion of interdigitated gel phase, together with an increase of the hydrogen bonding pattern of the interfacial region of the bilayer. In contrast, QM shows a weak interaction with the phospholipid bilayer. Molecular dynamics simulation indicates that TMCG locates in the interior of the bilayer, while QM is found interacting with the surface of the membrane. The observations are interpreted in terms of the mechanism of membrane prodrug activation and the underlying membrane perturbations of the biological actions of natural catechins.