Elder products are still underutilized sources of phytochemicals, mainly polyphenols, with extensive pharmacological effects on the human body. In this study, gingerbread cookies covered in chocolate (GC) were enriched with elderflower dry extract (EF) and juice concentrate (EB). The cookies (GC, GCEF, and GCEFEB) and the additives (EF and EB) were analyzed for total phenolic content (TPC), phenolic compound profile, antioxidant capacity (AC), and advanced glycation end products’ (AGEs) formation in both the free and bound phenolic fractions. Sensory analysis of the cookies was performed using an effective acceptance test (9-point hedonic scale), and purchase intent was evaluated using a 5-point scale. It was found that the flavonoid content was significantly increased (20–60%) when EF and EB were added to the cookies. Moreover, the EF addition to chocolate-covered GCs enhanced the content of phenolic acids (up to 28%) in the bound phenolic fraction. An increase in the AC values of enriched cookies was found, and the free phenolic fraction differed significantly in this regard. However, inhibition of AGEs by elder products was only observed in the bound phenolic fraction. In addition, EF and EB improved the overall acceptance of the cookies, mostly their taste and texture. Thus, elder products appear to be valuable additives to gingerbread cookies, providing good sensory quality and functional food characteristics.