The network of the Maillard reaction can be influenced by the presence of polyphenols. In this paper, we evaluated the ability of secoiridoids to interact with asparagine and lysine tuning the formation of dietary advanced glycation end-products (d-AGEs), dicarbonyls and acrylamide. Olive oil mill wastewater polyphenol powders (OMWP) were added to glucose and lysine or asparagine in silica model systems to mimic water activity present in cookies. Results revealed that acrylamide, Amadori compounds and N-ε-carboxyethyllysine (CEL) were reduced to 50%, after 13 min at 180 °C; for the reduction of N-ε-carboxymethyllysine (CML), secoiridoids were effective only in model systems with the addition of acacia fiber and maltodextrin as coating agents. In cookies, OMWP at three different concentrations decreased the concentration of protein bound Amadori compounds, CML, CEL and dicarbonyls. Acrylamide and 5-hydroxymethylfurfural were reduced to 60% and 76% respectively, highlighting the ability of secoiridoids-based functional ingredients in controlling d-AGEs formation.