This study had the objective of determining the effects of the addition of different ingredients and grape by-products (GP) to muffins on CML content. It was found that ingredients, such as salt, baking powder and protein-rich components, reduced CML from 50% to 86%. The use of all ingredients simultaneously caused the highest reduction in CML, suggesting synergistic effects in the muffin formula. Raw cane sugar produced higher amounts of CML than refined sucrose, probably due to metal-ion mediated degradation of fructoselysine. The CML content was correlated with the level of oleic acid at −0.829 and with the level of linoleic acid at 0.913. Muffins enriched with appropriate levels of GP (20%) showed a lowering of the CML level and no significant changes in the sensory profile. GP added to the model system with protein-rich ingredients resulted in the weakest inhibitory effects, probably due to the polyphenol–protein binding mechanism.