The capillary microreactor, with four stable operating flow patterns and a throughput range from g/h to kg/h, presents an attractive alternative to chip-based and microstructured reactors for lab and pilot scale applications. In this paper the extraction of 2-butanol from toluene under different flow patterns in a water/toluene flow in long capillary microreactors is presented. The influence of the capillary length (0.2-2.2 m), flow rate (0.1-12 ml/min) and aqueous-to-organic volumetric flow ratio (0.25-9) on the slug, bubbly, parallel and annular flow hydrodynamics was investigated. Weber number dependant flow maps were composed for capillary lengths of 0.4 and 2 m, which are used to interpret the flow pattern formation in terms of surface tension and inertia forces. By decreasing the capillary length from 2 to 0.4 m, the transition of annular to parallel flow was observed. The capillary length had little influence on the slug and bubbly flows. The flow patterns were evaluated in terms of stability, surface-to-volume ratio, achieved throughput and extraction efficiency. Slug and bubbly flow operation yielded 100 % thermodynamic extraction efficiency, while by increasing the aqueous-to-organic volumetric ratio to 9 allowed for 99 % 2-butanol extraction. The parallel and annular flow operational windows were limited by the capillary length, thus yielding maximal 2-butanol extraction of 30 and 47 %, for the parallel and annular flow, respectively.