Plasma seed treatment has proven to be a useful technique for improving germination, growth dynamics, as well as plant resistance. In this paper, we studied the efficacy of soybean seeds treatment using various sources of cold atmospheric pressure plasma generated in air. We compared three types of plasma treatments: direct treatment with plasma generated by a diffuse coplanar surface barrier discharge (DCSBD), direct treatment with plasma generated by a multi-hollow surface dielectric barrier discharge, and indirect treatment using the gaseous products of plasma generated by an air plasma jet. The composition of plasma generated by each of the sources was analysed using optical emission spectroscopy and Fourier Transform Infrared spectroscopy (FTIR). Parameters of the plasma treatments have been optimized to improve soybean germination. Plasma-treated seeds were examined by the means of water contact angle, surface free energy and imbibition measurements, attenuated total reflectance FTIR (ATR-FTIR), x-ray photoelectron spectroscopy (XPS) and scanning electron microscope (SEM) analyses. Surface analysis by ATR-FTIR and XPS showed changes in the chemical bonds on the surface of the plasma-treated seeds, which led to an increase in wettability and imbibition. SEM analysis confirmed that the plasma treatment is non-invasive and does not cause changes in seed surface morphology. Among the studied sources, DCSBD proved to be the best suited for soybean seed treatment in terms of germination improvement as well as treatment time and energy efficiency.