Application of plasma is well-established in various industrial processes; its use has also been suggested as an innovative technology in the food sector. Besides the ability to inactivate undesirable microorganisms on heat-sensitive foods, cold atmospheric pressure plasma (CAPP) may also modify and intensify the secondary metabolism in agricultural plant produces along the whole value-added chain. This is because CAPP provides a source of reactive oxygen and nitrogen species and specific UV radiation. The objective of this study was to determine the effects of CAPP treatment on the flavonol glycoside profile of pea seedlings (Pisum sativum ‘Salamanca’), while considering the potential impact on their metabolic activity in different growth stages. Pea seeds, sprouts, and seedlings were exposed to semi-direct CAPP using a dielectric barrier discharge device with air as the process gas. Applying voltages between 6 and 12kVpp at a frequency of 3.0kHz resulted in optical emission spectra dominated by UV-B and UV-C radiation. The specific energy densities were monitored upon varying voltages and treatment times. Exposing swollen pea seeds to plasma (9kVpp) between 1 and 10min increased germination rate and dry matter content but decreased growth rate. Non-acylated and monoacylated triglycosides of quercetin and kaempferol dominated the flavonol glycoside profile, quercetin-3-O-p-coumaroyl-triglucoside being the main flavonoid glycoside. In 15d-old pea seedlings, the concentration of flavonoid glycosides was dose-dependently decreased after two CAPP treatments compared to none or three treatments. Furthermore, photosynthetic efficiency of treated pea sprouts and seedlings declined potentially indicating a negative effect of CAPP treatment on plant metabolism. The responses of pea tissues greatly depended on time point and duration of CAPP treatments. This study represents a first step towards the implementation of the CAPP technology for a targeted modification of valuable secondary plant metabolites during post-harvest chain of agricultural produces. •The application of cold plasma during post-harvest processing of pea seeds was tested.•CAPP treatment affected the flavonol glycoside profile dose-dependently.•Plasma affects germination, growth and photosynthesis of pea sprouts and seedlings.•The applied CAPP was proven to be a source of UV-B and UV-C radiation.•An innovative process for the production of functional food is discussed.