In the current study, the effect of microwave pretreatment (MWP) at 180, 360 and 540 W for 5 and 10 min duration on black and white chia seed oil (ChO) quality, phenolic composition, and stability characteristics were investigated. Increase in MWP power and duration had increased the total phenolic and flavonoid contents, phenolic acids, flavonoids, tocopherols, pigments, oxidative stability, radical scavenging activity, ?E, a* value and browning index of ChO. The color attributes (L*, b*, chroma and hue values) were decreased by increasing MWP conditions. The 4-hydroxybenzaldehyde, hydroxybenzoic (vanillic, protocatechuic, ellagic and syringic acid), hydroxycinnamic (chlorogenic, rosmarinic, trans-cinnamic and caffeic acid) acids, and flavonoids (epicatechin, vitexin, rutin, myricetin and catechin) were highest in oil extracted after MWP at 540 W for 10 min. The increment in oxidative stability correlated significantly and positively with the level of phenolic acids, pigments, flavonoids and Maillard reaction products in ChO from microwave-pretreated chia seeds. The study concludes that the MWP of chia seeds at 540 W for 10 min had significantly improved the phenolic profile, radical scavenging activity, oxidative stability, and yield of ChO.