The presented study aims to experimentally investigate the potential of flash sanitation (short time exposure to hot air stream) for wheat seeds to control surface contamination and protect against fungal diseases. Experiments were conducted at the laboratory scale using very short residence times (2–4 s) and higher temperature range (150–350 °C) of dry air stream at two different flow rates (280 L/min and 557 L/min). The goal was to identify thermal conditions that provide high sanitation efficiency while maintaining seed viability. A design of the experiment approach, employing central-composite design and face-centred response surface methodology, was used to evaluate the effects of the thermal treatment on seed surface temperature, sanitation efficiency, and germination capabilities. Higher air flow rate (557 L/min) significantly increased post-treatment seed surface temperatures (42.1–122.7 °C) compared to the flow rate of 280 L/min (36.7–80.5 °C). Pronounced germination drops were observed with air temperatures above 175 °C. Satisfactory sanitation efficiency >90% was achieved only with high-temperature air >250 °C, which, however, caused unacceptable germination loss. Extending residence time beyond the experimental plan is unlikely to yield significant benefits, as the factor was identified as weak and insignificant compared to temperature. Higher flow rates improve heat transfer but require strict control to prevent variability affecting seed quality. The heating media flow rate should be considered an essential factor in thermal treatment studies. Dry air has not proven to be appropriate for seeds’ flash sanitation within the selected experimental condition framework.