Studying neuronal cells in space reveals how microgravity affects brain function, gene expression, and cellular processes. This study details the preparation and validation of a 3D neuronal electrophysiology (EPHYS) sensing microfluidic biodevice used during a suborbital space flight. Initially, the device’s function was tested with rat hippocampal neurons using EPHYS data collected via a microelectrode array (MEA). This system was later applied to human glutamatergic (Glu) neurons for eight days preceding a suborbital flight. A live-dead assay confirmed cell viability, and the system was integrated into a CubeLab to maintain a controlled environment. Two biological samples were flown, along with two control samples, to validate the EPHYS system. Results showed that human Glu-neurons exposed to microgravity exhibited altered expression of vesicular glutamate transporters (VGLUTs) while maintaining neuronal differentiation markers. The findings contribute to understanding neurological disorders, neuro-inflammation, and cognitive impacts of space travel, with broader applications for brain health research on Earth.