The development of organic biosignature analysis instruments with a high detection sensitivity is critical for exploring our solar system for habitability and for organic chemical biomarkers. In particular, the Microfluidic Organic Analyzer (MOA) has been developed in a compact, low-mass, space-flight compatible format to address this goal. To demonstrate the performance of the matured MOA instrument, we performed a series of five Zero-G parabolic aircraft flights to test the MOA microfluidic, capillary electrophoresis (CE) separation, and detection systems in micro- and hyper-gravity environments. Amino acid CE separations were performed in flight to develop the protocols and to determine the dependence of the separation quality on large variations in gravitational potential. We present here an amino acid separation performed as the gravitational potential varied from 0.16 to 1.7 g during the separation. The amino acid separation is essentially indistinguishable from separations performed in a constant 1 g environmental control. This work advances the technology readiness of microfabricated CE systems for planetary biosignature detection and enhances our preparedness for future flights.