A methodology based in flow analysis and membrane-based extraction has been applied to the determination of methanol in biodiesel samples. A hydrophilic membrane was used to perform the liquid-liquid extraction in the system with the organic sample fed to the donor side of the membrane and the methanol transfer to an aqueous acceptor buffer solution. The quantification of the methanol was then achieved in aqueous solution by the combined use of immobilised alcohol oxidase (AOD), soluble peroxidase and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS). The optimization of parameters such as the type of membrane, the groove volume and configuration of the membrane unit, the appropriate organic solvent, sample injection volume, as well as immobilised packed AOD reactor was performed. Two dynamic analytical working ranges were achieved, up to 0.015% and up to 0.200% (m/m) methanol concentrations, just by changing the volume of acceptor aqueous solution. Detection limits of 0.0002% (m/m) and 0.007% (m/m) methanol were estimated, respectively. The decision limit (CCalpha) and the detection capacity (CCbeta) were 0.206 and 0.211% (m/m), respectively. The developed methodology showed good precision, with a relative standard deviation (R.S.D.) <5.0% (n=10). Biodiesel samples from different sources were then directly analyzed without any sample pre-treatment. Statistical evaluation showed good compliance, for a 95% confidence level, between the results obtained with the flow system and those furnished by the gas chromatography reference method. The proposed methodology turns out to be more environmental friendly and cost-effective than the reference method.