Processed chocolate products often contain allergenic proteins that can trigger severe reactions in susceptible individuals. Chocolate components, such as polyphenols, tannins, and fat, as well as the physical texture of chocolate itself, can complicate the extraction and detection of allergenic proteins. Allergen detection is also affected by processing procedures that may result in physical and chemical interactions between chocolate matrix components and allergenic proteins. Allergen quantitation using commercial ELISA kits showed that peanut recovery was negatively impacted by the chocolate matrix and not by the tempering process, whereas milk allergen recovery was reduced after tempering. Egg allergen recovery was not affected by matrix components or tempering. To determine optimum protein extraction conditions, five different buffers were used to extract tempered and untempered chocolate. Qualitative comparison of different extracts by immunoblotting showed that detection problems associated with matrix components and processing effects may be overcome by the choice of sample extraction solution.