The nutritional quality of bakery products keeps on degrading from the process of baking, packaging, transportation and storage. The present study was carried out to evaluate the effect of addition of tomato powder (2 & 4/100 g of flour) and crude lycopene (50 & 100 mg/100 g of flour), which have potent antioxidant activity, on the nutritional quality and shelf life of cookies prepared from whole wheat flour. Color values i.e., a* and b* of freshly prepared cookies containing tomato powder (TP) were found in the range of 5.40–6.21 and 33.20–33.40 respectively, and that of crude lycopene (CL) in the range of 5.18–5.24 and 32.50–34.90 respectively, higher than the control (4.53 and 32.50, respectively). Significant (p < 0.05) and non-significant (p > 0.05) increase was observed in the total phenolic content of dough containing TP (0.54–0.72 mg GAE/g) and CL (0.46–0.59 mg GAE/g), when compared to control (0.38 mg GAE/g). Antioxidant properties like, DPPH scavenging activity, reducing power and inhibition of lipid peroxidation (ILP), and total carotenoid content (TCC) of dough and cookies increased significantly (p < 0.05) upon incorporation of TP and CL. Sensory properties of enriched cookies were comparable with that of control. Color values (a* and b*), hardness, TCC, ILP and TPC were reduced significantly (p < 0.05) with storage.