In this study, the effect of the addition of freeze-dried raspberry pomace on the content of phenolic compounds and the antioxidant and anti-inflammatory activity of wafers was investigated. Particular attention was paid to the biological activity of the potentially bioavailable fraction of polyphenols extracted via gastro-intestinal digestion. In the basic recipe for the waffle dough, flour was replaced with freeze-dried raspberry pomace in the amount of 10%, 20%, 30%, 50%, and 75%. The content of total phenolic compounds, phenolic acids, flavonoids, and anthocyanins in ethanol and buffer extracts and after in vitro digestion increased with the increase in the addition of pomace. A similar relationship was noted for antioxidant properties: ability to neutralize ABTS—2,2′-Azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) and DPPH—1,1-diphenyl-2-picrylhydrazyl radicals, iron II chelating ability, and reduction power. The extracts obtained after the simulated digestion showed the highest activities, which confirms that the polyphenols are a potentially bioavailable fraction. Extracts from the fortified wafers effectively inhibited the activity of enzymes involved in the generation of free radicals and induction of inflammation, i.e., xanthine oxidase (XO), lipoxygenase (LOX), and cyclooxygenase 2 (COX-2). The lowest IC50 values were determined for extracts after in vitro digestion. The sensory evaluation of the prepared wafers showed that the wafers fortified with 20% pomace achieved optimal scores. Enrichment of confectionery products with waste products from the fruit and vegetable industry can be a good way to increase the proportion of biologically active polyphenols in the diet and brings benefits to the environment.