Purpose: Weeds cause significant losses in agricultural production. In this study, we investigated the effect of microwaves on the germination rates of cress and arugula seeds to determine whether microwaves could be developed as an effective alternative to conventional chemical-based herbicides. Methods: Seeds were planted at equal depths (8-10 mm) in a soil-turf mixture, and seeds were exposed to microwaves for 126 s, 70 s, and 50 s in a device constructed specifically for this study. A microwave tunnel was built using a variable speed conveyor belt and 4 magnetrons with a combined output power of 2.8 kW. Seeds that were not exposed to microwaves were germinated with regulated irrigation, temperature, and humidity controls in parallel with the treated seeds, and the germination rates were compared among the treatment groups. Results: We found that the exposure of cress and arugula seeds to microwaves for 126 s inhibited germination close to 100%. Cress seeds treated with microwaves for 50 s showed 95% germination compared to 65% germination of the untreated cress seeds. Conclusions: We predict that the thermal effect of microwave energy affects the germination ratio and germination rate of seeds.