During harvesting, grain, straw, and cha with weed seeds are separated. The cha is returned to the fields, resulting in weed problems in the subsequent crops. We estimated the fraction of weed seeds a combine harvester could potentially harvest and used various methods to collect the cha and treat it with heat to kill weed seeds or reduce weed seed germination. Cha with weed seeds was placed on top of the straw and afterwards baled with the straw as a method to remove weed seeds from the field. We exposed cha with weed seeds to exhaust gas with various temperatures and durations to study whether this heating method could be used to reduce the input of viable weed seeds to the soil during harvesting. By collecting the shed weed seeds during the growing season, we estimated that a combine harvester could potentially harvest 41%, 11%, and 100% of the seeds produced in the growing season by Bromus hordeaceus, Cirsium arvense, and Galium aparine, respectively. When the cha was placed on top of the straw, 45% of the weed seeds stayed in the cha fraction on top of the straw swath after one day, 35% got into the straw swath, and 20% past through the swath to the ground. Therefore, baling straw with cha placed on the top only had a limited effect on reducing weed seed infestation. The study showed that thermal weed seed control during harvesting could potentially be applicable and incorporated in an integrated weed management approach.