Thylakoid membranes of photosynthetic plant chloroplasts are involved in a wide range of energy producing pathways. Their stacking can be employed in order to provide increased surface area for biocatalytic purposes. Here we probe the aggregate formation of higher plants' thylakoids using low-molecular poly-l-lysine as an electrostatic polymer linker in low ionic strength media. Microelectrophoresis, actinic light scattering, millisecond-delayed fluorescence and free radical production of thylakoid membranes are measured and analyzed in the presence of the cationic polypeptide to track its influence on the surface electrical properties, the electron-transport processes and the proton gradient accumulation across membranes. Enhanced proton gradient in polylysine-treated thylakoids is obtained upon illumination due to alterations of the proton intake across the membrane resulting from the non-specific electrostatic interactions of the cationic polypeptide with thylakoids. We report lower rates of lipid peroxidation in polylysine-treated thylakoids measured both in the dark and under illumination in salt-free medium. The gained insight on the effect of polycations on photosynthetic membranes may be used in future developments of thylakoid-based approaches for energy transfer applications.