Thin-film nanocomposite (TFN) membranes were prepared by embedding nano-porous SAPO-34 nanoparticles in a polypyrrole thin-film layer polymerized on PES substrate. SEM, EDX, AFM, hydrophilicity, zeta potential and MWCO measurements were applied to verify characteristics of membranes. TFN membranes presented considerably higher pure water permeability (by more than 300%) due to high hydrophilicity and also nano channels created in thin-film. Performance of TFN membranes were also evaluated by removal of different anionic and cationic dyes (methyl violet 6B, reactive blue 4 and acid blue 193) from water. TFN membranes effectively removed 100% of all dyes from feed aqueous solutions with a low concentration (50 mg/l). Moreover, TFN membrane prepared with the highest amount of nano-filler presented an elevated water flux in filtration of solutions containing each dyes (e.g. more than 500% for reactive blue 4), a reduced flux decline ratio (36%) and also a higher flux recovery ratio (85%) in comparison with the pristine thin-film membrane, consequently indicating high performance of TFN membranes and potential of recovery just after a simple water washing. TFN membranes also revealed an efficient performance in filtration of high concentrations of dye solutions as well as in treatment of a real wastewater produced by a weaving company.