BACKGROUND: As amino acids provide a green feedstock for the synthesis of chemicals, their isolation through low energy route sounds encouraging. RESULTS: The changes in the permeation characteristics ofmicrofiltration (MF) membranes with the deposition of a few bilayers of chitosan (CHI) and polystyrene sulfonate (PSS) for the low pressure filtration (similar to 0.69 bar) of selected amino acids glycine, histidine, lysine and aspartic acid is reported here. Glycine, with minimal electrostatic interaction with the multilayer film, is almost completely transmitted. Among the basic amino acids, lysine was isolated to a larger extent at both pI (pH 9.5, 7 bilayer, 67.8%) and below pI (pH 5, 7 bilayer, 96.4%). Aspartic acid was also isolated at both feed pHs (pH 5, 93.6%). Donnan effects operate in a different manner in both cases. At pH 5, lysine is adsorbed to the membrane as counter ions, whereas aspartic acid is excluded as co-ion fromthe film. The morphological features of membranes are illustrated through histogram, skewness, and Minkowski measures using AFM. CONCLUSIONS: The present study brings forward the possibility of cutting down the filtration pressure to a lower value for the isolation of small molecules like amino acids by water based coating of a few bilayers on MF membranes. (C) 2016 Society of Chemical Industry