Shortbread biscuits have become one of the most desirable snacks in all population groups but due to its high fat content it is searching for new solutions of fat reduction such as the use of carbohydrate-based fat mimetics. However, the thermal processing of food containing lipids in the presence of certain carbohydrates can contribute to the formation of toxic compounds or alter its levels. Therefore, the aim of the study was to evaluate the use of inulin and pectin gels as partial fat replacers (10–40%) in classical shortbread biscuits in a view of the changes of 3-monochloropropane-1,2-diol ester (3-MCPDE) and glycidyl ester (GE) levels after baking, and also after a two-months storage. The experiment showed that the amount of inulin gel higher than 10% promoted the endogenous formation of 3-MCPDE probably due to the higher amount of Maillard products formed in the biscuits, but after two months the levels decreased and were comparable with those transferred from shortening. Pectin did not demonstrate such phenomenon, owing to the presence of bound water in gel. Glycidyl esters were partially decomposed during baking and also during storage, particularly in the samples with the addition of pectin gel, which presumably caused by low stability of GE under acidic conditions resulting from the occurrence of galacturonic acid in pectin.