Sesame (Sesamum indicum) seeds are highly valued for their culinary applications and for producing a premium-quality oil. This study investigated the polyphenol content and fatty acid composition of a set of sesame accessions and examined their association with seed colors. Among the different colors, black-seeded accessions exhibited the highest total lignan content, while white-seeded accessions had average lower levels. Brown-seeded accessions showed relatively lower concentrations of sesamol and intermediate levels of sesamolin and sesamin than other colors. The oil derived from these seeds contained unsaturated fatty acids (UFAs) and saturated fatty acids (SFAs), nutritionally crucial for human consumption. Brown varieties exhibited higher concentrations of these fatty acids. Roasting black and white sesame seeds at increasing temperatures (180 and 250 °C) significantly affected lignan and UFAs concentrations. Higher temperatures resulted in elevated levels of detrimental t-oleic and t-linoleic acids. Furthermore, sesamolin content notably decreased at 180 °C and became undetectable at 250 °C. The temperature also caused a marked increase in sesamol, regardless of seed color. PCA analysis highlighted clusters between white and black varieties according to roasting temperature, displaying the potential application of chemometrics to assess processing effects and ensure sesame quality and safety. This research provides valuable insights for exploiting sesame within agrosystems in Mediterranean climates.