Unmanned Aerial Vehicles (UAVs) are becoming increasingly popular thanks to an increase in the accessibility of components with high reliability and reduced cost, making them suitable for civil, military and research purposes. Vehicles classified as UAVs can have largely different properties in terms of physical design, size, power, capabilities, as well as associated production and operational cost. In this work, we target UAVs that feature a high number of degrees of freedom (DOF) and that are instrumented with a large number of sensors. For such platforms, we propose an architecture to perform data acquisition from on-board instrumentation at a frequency (100 Hz) that is twice as fast as existing products. Our architecture is capable of performing acquisition with strict timing constraints, thus, the produced data stream is suitable for performing real-time sensor fusion. Furthermore, our architecture can be implemented using embedded, commercial hardware, resulting in a low-cost solution. Finally, the resulting data acquisition unit features a low-power consumption, allowing it to operate for two to three hours with a miniature battery.