Formation of Maillard reaction products (MRPs) including 5-hydroxymethylfurfural (HMF) and acrylamide has been an intensive area of research in recent decades. The presence of reactants such as sodium chloride may influence the Maillard reaction (MR) pathways through the dehydration of various key intermediates. The aim of this work was to test the potential of ingredient encapsulation to mitigate the MR by investigating the case of sodium chloride encapsulation on the HMF formation in cookies. Thirteen cookies were prepared with recipes containing free or encapsulated NaCl. Increasing NaCl concentration from 0 to 0.65% increases HMF concentration up to 75%, whereas in the presence of encapsulated NaCl the reduction of HMF varied from 18 to 61% due to the inhibition of sucrose pyrolytic decomposition and the fructofuranosyl cation formation. Data demonstrated that the more heat-resistant the lipid-based coating was, the more pronounced the reduction of HMF formation. The results showed that encapsulation represents a useful approach to prevent the formation of potentially harmful compounds in thermally processed foods.