Gluten-free foods (GF) availability on supermarket shelves is growing and it is expected to continue expanding in the years ahead. These foods have been linked to a lower content of fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAPs), molecules that trigger gastrointestinal symptoms in sensitive persons. In this study, the FODMAP content of 25 cereal-based GF foods in Spain (breakfast cereals, pasta, bread, biscuits, bakery products, and dough and puff pastry) and 25 gluten-containing equivalents (GC) available in the same supermarket were analysed and compared. Lactose, fructose, glucose, sorbitol, mannitol, raffinose, stachyose and fructans were quantified. In a like-by-like analysis, GF foods were found to generally contain fewer FODMAPs than their GC counterparts. The ingredients used in the manufacture of GF cereal-based foods may contribute to this fact. When the individually wrapped size was considered, the proportion of samples classified as high-FODMAPs in GC and GF foods showed a trend towards fewer samples in the GF. However, not all the GF samples were low-FODMAP. Altogether, our findings provide essential information for FODMAP content databases of GF products in Spain.