Treatment of plant seeds with electromagnetic fields or non-thermal plasmas aims to take advantage of plant functional plasticity towards stimulation of plant agricultural performance. In this study, the effects of pre-sowing seed treatment using 200 Pa vacuum (7 min), 5.28 MHz radio-frequency cold plasma (CP −2, 5, and 7 min) and electromagnetic field (EMF −5, 10, 15 min) on seed germination kinetics, content of phytohormones, morphometric parameters of seedlings and leaf proteome were assessed. CP 7 min and EMF 15 min treatments caused 19–24% faster germination in vitro; germination in the substrate was accelerated by vacuum (9%) and EMF 15 min (17%). The stressors did not change the seed germination percentage, with exception of EMF 5 min treatment that caused a decrease by 7.5%. Meanwhile both CP 7 min and EMF 15 min treatments stimulated germination, but the EMF treatment resulted in higher weight of leaves. Stressor-specific changes in phytohormone balance were detected in seeds: vacuum treatment decreased zeatin amount by 39%; CP treatments substantially increased gibberellin content, but other effects strongly varied with the treatment duration; the abscisic acid content was reduced by 55–60% after the EMF treatment. Analysis of the proteome showed that short exposure of seeds to the EMF or CP induced a similar long-term effect on gene expression in leaves, mostly stimulating expression of proteins involved in photosynthetic processes and their regulation.