Twenty-eight populations of ajowan (Trachyspermum ammi L.) were evaluated for morphological traits and oil yield in two consecutive years. Then, selected ajowan populations that revealed medium and high oil yield and higher seed weight in two years were selected for further studies. These were assessed for physiological traits, total phenolic and flavonoid contents and antioxidant capacity under four salt treatments control, 60, 90, and 120 mM NaCl. The essential oil composition was analyzed by gas chromatography-mass spectrometry (GC-MS) Thymol (32.7-54.29%), γ -terpinene (21.71–32.81%), and p-cymene (18.74–26.16%) were major components. The highest and lowest thymol were recorded for Qazvin (control) and Qazvin (Low salt concentration), respectively. Salt stress caused an increase in essential oil content of Esfahfo and Qazvin populations. The highest phenolic and flavonoid contents were found in Arak population grown in 60 mM NaCl (183.83 mg TAE g− 1 DW) and Yazd population grown in 90 mM NaCl (5.94 mg QE g− 1 DW). Moreover, Yazd population exhibited the strongest antioxidant activity based on DPPH (IC50 = 1566µg/mL) under 60 mM NaCl and the highest reducing power (0.69 nm) under 120 mM NaCl. Overall, the results revealed that low and moderate salt stress improves the phytochemicals of ajowan, being especially useful for pharmaceutical and food applications.