To meet the needs of the hungry population, it is critical to boost agricultural product production while minimizing contaminated waste. The use of two nonthermal technologies, pulsed electric field (PEF) and nonthermal plasma (NTP), is increasing every day. As both PEF and NTP are relatively newer areas, there is limited knowledge about these two technologies and their modes of action. Studies showed that PEF treatment on the plant seeds helps germination and seedling growth. The positive impact of PEF intensity is highly dependent on the seed coat type and plant species. Another nonthermal technology, NTP, affects seed germination, seedling growth, yield, and resilience to abiotic stress when generated at varying pressures with and without different feed gases. Early germination, germination rate, and germination percentage were all improved when the seedlings were treated with NTP. Similarly to the PEF treatment, NTP had a negative or no effect on germination. This review examined the effects of PEF and NTP on seed germination and analyzed the situation and mechanism behind the positive or negative effect. Deactivation of proteins and enzymes to extend the shelf life of beverages is another prominent application of PEF and NTP. The interaction of PEF and NTP with proteins aids in understanding the microscopic mechanism of these technologies. Therefore, we covered in this review the potential structural and functional changes in proteins/enzymes as a result of PEF and NTP, as well as a comparison of the benefits and drawbacks of these two technologies.