To improve the process of seed extraction, new solutions have been investigated in an attempt to develop guidelines for the construction of small seed extraction equipment. One of the solutions proposed in this field is the use of electromagnetic radiation in the first stage of hulling cones, reducing their initial moisture content, which will result in quicker scale opening. It is proposed that cones should be irradiated for a relatively short period in the first stage. This operation will allow a quicker loss of moisture from the cones that are still closed, which will result in a more intensive opening of cone scales and will also positively affect the exposure of seeds for the next phase of hulling. The aim of the study was to evaluate the effect of microwave irradiation of pine cones on the quality of the seeds obtained. Cones were exposed to microwaves produced by an 800 W generator. The research was performed in several modes, in which the variable parameters were the duration of microwave irradiation, arrangement of cones with the apex pointed towards either the inner or outer part of the turntable, and the number of cones. The temperature distribution on the surface of and inside the cones was determined using the THERM v2 (Vigo System SA, O(z) over dotarow Mazowiecki, Poland) thermal image processing software. We also assessed the energy (vitality) and germinability (quality class) of seeds that were not exposed and those after microwave treatment. The results of the research allowed us to state that, with the assumed parameters of the process, it is possible to obtain second quality class seeds after exposure to microwaves for 5 s. This result was comparable to the quality of seeds obtained without the use of microwaves. When the irradiation time was increased above 5 s, the vitality of seeds decreased and their quality was not satisfactory.