Fruit pomace, as a by-product of fruit and vegetable processing, is a cheap and easily accessible material for further processing that can replace selected recipe ingredients, most often flour. In addition, their advantage is their high health-promoting potential. The aim of this study was to evaluate the effect of the simultaneous use of erythritol (100% sucrose substitution) and the addition of varying amounts of blackcurrant, chokeberry and apple pomace (0%, 10%, 30% and 50% by weight of flour) on the glycaemic response after consumption of shortbread cookies in an in vivo study with humans (ISO 26642:2010). It was shown that an increase in the addition of each type of pomace reduced the glycaemic index value of the cookies. The pomace and sucrose-sweetened cookies were classified in the medium and low GI group. For each type of pomace, an increase in its share in the recipe of cookies was associated with a reduction in GI values (pomace: apple 49.1–37.2%, blackcurrant 56.4–41.0%, chokeberry 59.4–35.5%). Similar correlations were shown for the use of erythritol (pomace: apple 39.5–29.1%, blackcurrant 43.9–31.9%, chokeberry 34.6–20.7%). A significant effect of pomace addition on the GI values of shortbread cookies, was only observed for sucrose-sweetened products. The results obtained allow the conclusion that there is potential for the use of waste raw materials in the production of functional foods.