Plasma-activated water (PAW) is an emerging and promising green technology in the agriculture sector during recent years. The aim of this study was to examine the influence of the spraying of PAW and amino acid fertilizer concentrations on the physiological, biochemical and phytochemical characteristics of German chamomile varieties under field conditions. Method: The experiment was performed during 2020–2021 as a factorial using a randomized complete block design with three replications, in an arid and warm region. The factors contained five fertilizer levels (0 (control), 1, 2, 3 ml·L−1 amino acid and PAW) and three German chamomile cultivars Bona, Bodegold, Lianka). Physiological, biochemical and phytochemical traits such as plant height, fresh and dried flower weight, chlorophyll a, b, carotenoids, CHN elements, C:N ratio, total protein, amino acid profile, essential oil yield, apigenin content and major secondary metabolites were examined. Results: The ANOVA indicated that the impact of the cultivar and fertilizer was significant on all physiological, biochemical and phytochemical studied parameters. The amino acid fertilizer and PAW enhanced physiological features, hydrogen, C:N ratio, essential oil yield, apigenin content and main phytochemical compositions like chamazulene and α-bisabolol, but it had no incremental effect on the carbon, nitrogen, and total protein percentage. Conclusion: Findings revealed that the application of foliar amino acid fertilizer and PAW treatments improves physiological, biochemical and phytochemical parameters in German chamomile cultivars under field conditions.