The publication describes research investigating the effects of microwaves on seeds extracted from Norway spruce (Picea abies) and European larch (Larix decidua) cones. The objective of the conducted experiments was to determine how electromagnetic radiation influences the quality of those seeds. The study material was heated in a microwave-emitting device for 7 or 10 s at four power settings (800, 620, 440, or 130 W). The evaluated parameters included changes in the moisture content and weight of the studied cones following the applied time and power variants of exposure to microwaves, as well as the quality of the obtained seeds expressed in terms of germination energy (GE) and capacity (GC). Increasing the power of microwaves resulted in a greater decrease in the moisture content of cones, but it was not possible to find such a relationship for larch cones, especially for large cones. In most cases, the irradiation of larch cones with electromagnetic waves resulted in class I seeds, in contrast to spruce seeds, which could not be assigned to any class. Our findings show that for optimum results larch cones may be exposed to microwaves at a power not greater than 620 W and for a time not longer than 10 s. Spruce cones were found to be very sensitive to radiation; in their case no microwave treatment should be applied as it adversely affects seed viability.