Microwave processing (MwP) is an energy-efficient and impressive method for modifying the functional properties and enhancing the availability of nutrients and bioactive constituents in flaxseeds (FS). The comprehensive and comparative evaluation of FS flour and flaxseed press cake (FPC) flour after MwP is required for large-scale industrial processing and utilization of flaxseeds. In this study, the changes in phenolic composition, Maillard products, physicochemical and functional properties of FS flour and FPC flour after MwP of flaxseeds at 180 W, 360 W, and 540 W for 5, 10, and 15 min were investigated. The unprocessed FS and FPC flour differed in the level of ash, fat, minerals, phenolics, flavonoids, and functional properties. The oil absorption capacity, protein, zinc, and copper augmented in FPC flour and declined in FS flour upon increasing MwP conditions. The phenolic acids (free gallic, protocatechuic, syringic, and caffeic acid, bound protocatechuic and vanillic acid), flavonoids (free rutin, bound epicatechin, and kaempferol), Maillard products, and browning index augmented in FS and FPC flours upon MwP at 540 W for 15 min. However, the L* and b* values, magnesium, potassium, selenium, bound catechin, free epicatechin, and free quercetin declined in FS and FPC flours upon MwP at higher power and time. The FPC flour obtained after MwP at 540 W for 15 min exhibited higher ash (5.71 %), protein (29.46 %), and water absorption (7.17 g/g), lowest emulsifying activity (20.03 m2/g), emulsifying stability (14.66 min) and water solubility (3.95 %) indexes. While the FS flour obtained upon MwP at 540 W for 15 min showed the highest fat content (37.52 %) and water solubility (6.20 %), lowest protein content (24.03 %), minerals, color values, oil absorption (1.69 g/g), emulsifying activity (41.38 m2/g) and stability (21.82 min). In conclusion, the MwP of flaxseeds can be used in industries to improve phenolic profile, Maillard products and modify functional properties of FS and FPC flour for possible utilization in food products.