Microfluidic liquid-liquid extraction of the ethyl ester of docosahexaenoic acid (DHA-Et) with silver ions was investigated using slug flow and a water-in-oil (W/O) emulsion as specific flow patterns possessing large interfacial areas. To compare the extraction rates of both systems, slug flow and a W/O emulsion with similar specific interfacial areas were prepared. Extraction rates for the systems were the same at 298 K However, at 268 K, slug flow had a faster extraction rate than the W/O emulsion. Theoretical calculation follows the results for both systems at 298 K and for the slug flow system at 268 K, suggesting that the emulsion stabilizer inhibits complex formation between DHA-Et and silver ions at the O/W interface. A reduction in extraction rate was observed in the slug flow system at 268 K when the emulsion stabilizer was used. Slug flow can be prepared without stabilizer, offering advantages over emulsions in microfluidic extraction.