Environmental stressors on the agricultural field are increasing, from global warming to the rise of the human population. Among the resulting challenges, plant diseases remain one of the most important causes of crop losses worldwide. Chemical pesticides are used to protect crops, yet they often come with significant environmental risks to the farmers, water, pollinators, and soil diversity. It is crucial, therefore, to investigate non-chemical alternatives to protect crops. Nevertheless, their effectiveness often varies and is difficult to predict, as results obtained under laboratory conditions rarely translate to the complex and dynamic environments of agricultural fields. In this 3-year on-farm study, we compared the effects of chemical and alternative seed treatments (Thermoseed, electron beam, and mustard-based treatments) on agronomic parameters (yield, protein, thousand grain weight, and micronutrients) as well as on the bacterial and fungal microbial communities associated with winter wheat. Neither the chemical nor the alternative seed treatments affected any of the agronomic parameters measured. The treatments had no effect on the microbial community. Because the seeds used had a low disease prevalence, it was not possible to assess the intrinsic efficacy of the alternative treatments. The alternative treatments showed no evidence of phytotoxicity in our on-farm field study, indicating their suitability for further evaluation. However, none of the treatments, including the synthetic treatment, had a positive effect when seeds carried a low pathogen load. Our results suggest that pesticide applications on seeds with low levels of seedborne pathogens may be unnecessary, unless soilborne pathogens are suspected to be present.