Replacing sodium chloride by salt substitutes in the recipe is one of the main strategies applied in the food industries to prevent unwanted health effects into population. However the reduction in NaCl may affect to the oxidative balance and the formation of process contaminants in the food, besides of sensorial and technological aspects already known. The effect of replacing NaCl by different salts and two commercial salt-replacers on the formation of acrylamide and furfurals, as well as the influence on the lipid oxidation after storage was evaluated in a cookie model. Acrylamide content was reduced by up to 58% in the cookie containing CaCl2 and 35–40% when NaCl was partly substituted by commercial salt-replacers. Hydroxymethylfurfural and furfural content did not greatly varied by the recipe, except by CaCl2, which significantly increased the furfurals formation. Although no significant relationship was found between mineral composition and lipid oxidation after storage, products of lipids oxidation were detected. In conclusion, the type of salts used in the cookie recipe affects the extent of lipid oxidation and the formation of process contaminants and, therefore, these potential side effects should be carefully considered by the food industries when implementing sodium reduction strategies in their products.