Chia seed ( L.) is a food rich in protein, fiber, polyunsaturated fatty acids and antioxidants. Consequently, its incorporation in food formulations may be desirable from a nutritional and healthy point of view. However, there is concern regarding the formation of process contaminants when they are subjected to thermal processing. The objective of this study was to incorporate different amounts of ground chia seeds in a biscuit model to evaluate the effect on the antioxidant capacity and formation of acrylamide and furfurals. Seven standard "Maria-type" biscuit formulations were prepared, replacing wheat flour with different amounts of ground chia seeds (defatted and non-defatted), from 0% (control biscuit) to 15% (respect to total solids in the recipe). Samples were baked at 180 °C for 22 min. Compared with the control biscuit, chia formulations increased the content of nutrients, antioxidant capacity (ABTS) and phenolic compounds (Folin-Ciocalteau method) but also doubled acrylamide levels and even raised more than 10 times furanic compound concentrations. Results indicate that the use of chia seeds as ingredients in new cereal-based formulations would improve the nutritional profile but also increase the occurrence of chemical process contaminants. This paradox should be carefully considered in the context of risk/benefit analysis.