Coffee is the most consumed beverage in the world, and in the form of instant coffee, it is highly appreciated for its ease of use. However, its frequent consumption may cause side effects like hypertension and arrhythmias due to the presence of caffeine. For this reason, decaffeinated coffee has become more popular. The decaffeination process affects both the chemical and nutritional profile. This study aimed to investigate these differences to evaluate nutritional aspects as well as the presence of descriptors for authentication issues. Six commercial brands (three decaffeinated and three normal instant brands of coffee) were analyzed for their fatty acid and tocopherol profiles by GC-FID and UHPLC-FLR, respectively. Four saturated fatty acids, three monounsaturated fatty acids, and two polyunsaturated fatty acids were identified. The most abundant were C16:0, C18:2, C18:0, and C18:1. α and β tocopherols were the only ones identified, with a total concentration ranging from 78 to 789 mg/kg in decaffeinated coffee and from 63 to 428 mg/kg in normal instant coffee. From the statistical analysis, β tocopherol registered the highest VIP score (3.5). While the t-test showed that C18:1 was statistically different (p< 0.05) between the normal and instant coffees, no statistical difference was observed for β tocopherol in both coffee types. For this purpose, C18:1 could be a potential marker for discriminating between normal and decaffeinated instant coffees. Further research needs to be carried out to confirm these results.