Many studies show that in the last 20 years, the increase in production per hectare has been achieved mainly due to the creation of new varieties and the development of plant breeding. Innovations in plant breeding are the main way to find new traits, values and tolerances, which are the only ones that can respond to the increased demand for yield and more efficient production. In addition to high and stable yields, it is very important that the soybean seed has a satisfactory technological quality. Therefore, the aim of this study was to examine how the application of pulsed electromagnetic fields (PEMFs) affected the protein yield of soybean seed depending on the year, exposure time and frequency. The field trials were conducted in the experimental field of the Institute of Field and Vegetable Crops in Novi Sad, Serbiain 2010–2013. For this research, the seeds of a medium-sized variety Valjevka exposed to a pulsed electromagnetic field (PEMF) using a pulse generator and a strip applicator were used. A low frequency pulsed electromagnetic field (16, 24, 30, 72 Hz) was used at the exposure times of 0, 30, 60, and 90 minutes. The results of the research show that the application of this method can increase the yield of protein in soybean seed for more than 20%, which is a significant increase, especially in organic production, where the use of seed treatment agents is very restricted. However, this measure can also have an inhibitory effect if an adverse combination of exposure time and frequency strength is selected.