The discrepancies between reality and simulation impede the optimization and scalability of solid-state quantum devices. Disorder induced by the unpredictable distribution of material defects is one of the major contributions to the reality gap. We bridge this gap using physics-aware machine learning, in particular, using an approach combining a physical model, deep learning, Gaussian random field, and Bayesian inference. This approach enables us to infer the disorder potential of a nanoscale electronic device from electron-transport data. This inference is validated by verifying the algorithm’s predictions about the gate-voltage values required for a laterally defined quantum-dot device in AlGaAs/GaAs to produce current features corresponding to a double-quantum-dot regime.