The aim of this paper is to present an alternative to conventional biodiesel production by taking advantage of the flow patterns formed in micro-reactors. Biodiesel production was carried out 15 times faster in a tubular micro-reactor (TMR) than a well-mixed batch reactor (BR), achieving conversions up to approximate to 99% with 4 min of residence time. The experimental results were analyzed using dimensionless numbers and computational fluid dynamics (CFD) simulations. The CFD results showed that under the conditions used in the present study, the slug flow pattern can be expected, and this could explain the high conversion (>90%) reached in the TMR without using high methanol-oil molar ratios. The internal movement (auto-mixing) in the slug enhanced the mass transfer. Moreover, CFD simulations showed that at low conversion (<25%), the internal velocity of the oil slug will be the key factor related to the reactor performance.