Chia (Salvia hispanica L.) is an emerging crop with a high content of α-linolenic acid and metabolites of industrial and pharmaceutical interest but information on metabolome variations in response to agricultural management is scarce. We investigated the yield and metabolic profile of the seeds of two chia populations, one commercial black (B) and one long-day flowering genotype (G8), in response to two irrigation levels: replacement of 100% ET0 (I) or rainfed (NI). Seed yield was higher in irrigated plots in G8 only (0.255kgm−2 for I vs 0.184kgm−2 for NI) while it was very low regardless of irrigation in B due to late flowering. Ultrasound assisted extraction (UAE) of seeds followed by gas chromatography-mass spectrometry (GC/MS) analysis showed differences in fatty acids and the major classes of organic compounds due to both genotype and irrigation, especially in the non-polar phase where irrigated samples showed a higher content of α-linolenic and other fatty acids and a lower oleic/linoleic ratio (47.4 in NI vs. 39.6 in I). The antioxidant activity, expressed as trolox equivalent antioxidant capacity (TEAC), ranged from 1.317±0.027 to 2.174±0.010mmol TEAC/g of defatted chia seed after 2 and 40min respectively, and was negatively affected by irrigation. The total polyphenolic content (TPC) measured with the Folin-Ciocalteu method, also decreased with irrigation. According to our results irrigation can affect chia yield, metabolome and antioxidant behavior but some of the effects are genotype-dependent.