In this study, the effect of temperature (160–180 °C) and time (15–35 min) on functional properties, antioxidant activity, total phenolic content, the fatty acid composition of chia seed (Salvia hispanica L) flours were evaluated. Results showed roasting significantly increased the oil absorption capacity, water absorption index, water solubility index, water absorption capacity, and browning index and decreased moisture content of flours. Omega-3 (α-linoleic acid) was the main fatty acid detected in both raw and roasted chia seed flours followed with linoleic and oleic acids. Based on obtained results, at 180 °C, increasing the roasting time (15 to 25 min) significantly decreased the amount of chlorogenic acid and pyrocatechol from 0.15 (mg/g) and 1.5 (mg/g) in the raw sample to 0.11 (mg/g) and 1.25 (mg/g) in the chia seed flours roasted at 180 °C for 25 min, respectively. Fourier-transform infrared spectra showed roasting reduced the amount of polysaccharide (1740–1750 cm−1) and protein/lipid (2800–3000 cm−1) in samples. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis photograph showed roasting reduced the amounts of globulins S 7 and S 11 of chia seed flours. The current study explains the roasting at 180 °C for 35 min improved functional properties and total phenol content of chia seed flours.