Freeze-dried elderberry and chokeberry were proposed as natural colorants for gluten-free wafers. In addition to colour, other physical and sensorial properties of wafer sheets were also evaluated. The elderberry powder was significantly darker (L* equal 37.61) than the chokeberry powder (L* equal 41.01), and it was characterized by a considerably lower a* value (4.21 in comparison with 12.32). These powdered fruits were added in the range from 0 to 5 %. A new indicator of wafer batter delamination was developed, which can also be proposed for other liquids. Significant and favourable changes were noted in the colour of both batter and wafers, with an increased content of fruits from 1 to 5%. Gluten-free wafers with a 5% addition of fruits were characterized by L*, a*, b* values, respectively, equalling 35.73, 6.05 and 3.24 for elderberry, and 39.74, 7.15 and 5.05 for chokeberry. Wafers with a 5% addition of chokeberry and elderberry, in comparison to control wafers, had significantly higher contents of minerals, including iron, potassium, calcium, magnesium and sodium. The freeze-dried elderberry powder, as compared to the chokeberry powder, was found to significantly increase the content of these minerals. In addition, the total flavonoids content was higher in the wafers containing elderberry. Freeze-dried chokeberry and elderberry can be proposed as natural colorants and valuable functional components for wafers.