Fischer–Tropsch synthesis (FTS) was carried out in a water/oil mixture medium, using a Ru catalyst supported on a multi-walled carbon nanotube/MgO–Al2O3 hybrid as a catalyst support. The nanohybrid particles at the water/oil interface facilitated and stabilized the formation of water-in-oil emulsion, giving rise to an oil/emulsion/water trilayer liquid structure. FTS occurred at the emulsion phase with much higher conversion rates than those in oil single-phase reactions, yielding products with Anderson–Schulz–Flory distribution. Alkane-enriched hydrocarbons migrate to the top oil phase, while short alcohols remain in the bottom water phase. Thus, this multiphase liquid structure facilitates the separation of products according to their solubility in different phases. This significant advantage of combined reaction and separation is unique to the multiphasic system. In addition, differences in solubility could be used to enhance tolerance against impurities and catalyst poisons in the syngas feedstock. As a preliminary case study, hydrochloric acid and pyridine were chosen as model contaminants commonly found in biosyngas. It was found that their presence did not affect the catalytic activity as severely as could be expected in a conventional FTS process. Thus, emulsion-phase FTS could be beneficial to operations where syngas production such as biomass gasification and FTS are integrated. The several advantages of using emulsion systems in FTS are discussed in light of the current results.