Ethylene oxide (EtO) sterilization is commonly used by the food industry to inactivate pathogens in spices, but its efficacy on edible seeds, a high-risk food commodity, remains unexplored. This study aimed to evaluate the antimicrobial efficacy of EtO gas on chia seeds and assess the impact of processing parameters on microbial reduction, byproduct formation, and seed quality. Further, Enterococcus faecium NRRL B-2354 was evaluated for its suitability as a surrogate for Salmonella. Chia seeds were inoculated with a cocktail of five strains of Salmonella enterica or E. faecium. The inoculated sample was treated with EtO (735.3 mg/L) at different combinations of relative humidity (30, 40, and 50%) and temperature (46, 53, and 60 °C) for exposure times ranging from 2 to 120 min. The results showed that EtO treatment effectively reduced the bacterial populations on chia seeds, with the inactivation trend following a non-linear pattern that was described well by the Weibull model. The treatment time required for a 5-log reduction of Salmonella was less than 10 min at 50% RH and 53–60 °C. Exposure of chia seeds to EtO for 2 min at 50% RH gave 3.15, 3.59, and 3.87 log reductions at 46, 53, and 60 °C, respectively. E. faecium was found to be a reliable surrogate for Salmonella during EtO treatment. The modified Bigelow model developed based on Weibull model parameters could be used to predict Salmonella inactivation (RMSE = 0.73 min) and E. faecium inactivation (RMSE = 0.87 min) on chia seeds during EtO treatment. Fatty acid composition, protein content, color, and germination ability of chia seeds were not impacted significantly (P > 0.05) by EtO fumigation. These findings suggest that EtO gas can effectively inactivate Salmonella on chia seeds while preserving their viability and quality.