Since there are no products in the European market labelled as low-FODMAP (low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols), patients with irritable bowel syndrome and non-celiac wheat sensitivity often consume gluten-free products. These naturally contain little FODMAP, but have poorer sensory properties and lower nutritional value. This study aimed to develop sensory attractive crackers with high-fibre and low-FODMAP content. Various gluten-free flours (wholemeal buckwheat and millet, white maize), pumpkin seed meal, chia seeds, flax seeds, rice protein, sweet potato, sourdough, and spices were used to develop nine formulations. Using a nine-point hedonic scale and ranking test, four best-scored products were selected for which descriptive sensory analysis was performed and nutritional value and fructan content were determined. Crackers made from maize and millet flour mixtures (ratio 1:2.5) with sourdough and with chia or flax seed addition were rated highest for overall impression (8.2 and 7.0, respectively). Generally, high-fibre content, hardness, chewiness, dark colour, and bitterness lower the acceptability of crackers, but the addition of spices and sourdough can improve their acceptability and marketability. The crackers could be labelled as “gluten-free”, “low-FODMAP” (<0.12 g/100 g), “naturally high-fibre” (7–10 g/100 g of which 17–23% are soluble), and “high in protein” (24–26 g/100 g).