Sugar beet molasses is a raw material with high potential to be a functional ingredient in baked goods. This paper investigated the nutritional and functional properties of gluten-free cookies enriched with sugar beet molasses. At all enrichment levels and forms tested (liquid and dry), the addition of beet molasses improved the micronutrient pattern and antioxidative status of gluten-free cookies. The cookies prepared with molasses were significantly higher in potassium, magnesium, calcium, iron, betaine, total phenolics and DPPH radical scavenging abilities. Molasses contributed to wider spectra of phenolic compounds. The dominating phenolic compounds in the molasses-enriched cookies were catechin, ferulic, syringic and vanillic acid. Molasses also contributed to the presence of p-hydroxybenzoic acid in the cookies. Addition of molasses increased the content of hydroxymethyfurfural in the cookies, but not above values commonly reported for this product type. Molasses addition improved the overall acceptance of gluten-free cookies up to 30% enrichment level.