A one-stage syngas-to-fuel process was carried out by integrating Fischer-Tropsch synthesis (FTS) with hydrocracking (HC) in a micro-reactor to verify the feasibility of a related process simplification with a view to small-scale X-to-liquid (XtL) plants. Different approaches to the integration of the two process steps and the influence of the operating conditions were investigated targeting liquid fuel synthesis (C5–C20). It was proven that FTS plays the determining role in the integrated process and HC only exhibits a promoting function. Good performance was obtained in both sequential and mixed-bed systems. With an increase of temperature the liquid fuel selectivity reaches a plateau value of around 70% at 230–250°C, depending on the integration pattern and syngas space velocity. H2/CO ratio and pressure only have limited influence on the fuel selectivity. FTS was enhanced in the mixed-bed configuration. Meanwhile, consistent hydrocarbon distribution was obtained for both integration patterns when reaching the plateau fuel selectivity. The catalyst stability in both configurations was analyzed, and a reasonable and comparable long-term stability was obtained.