Immunodetection of allergens in dark chocolate is complicated by interference from the chocolate components. The objectives of this study were to establish reference materials for detecting multiple allergens in dark chocolate and to determine the accuracy and precision of allergen detection by enzyme-linked immunosorbent assay (ELISA) before and after chocolate processing. Defatted peanut flour, whole egg powder, and spray-dried milk were added to melted chocolate at seven incurred levels and tempered for 4 h. Allergen concentrations were measured using commercial ELISA kits. Tempering decreased the detection of casein and β-lactoglobulin (BLG), but had no significant effect on the detection of peanut and egg. Total coefficients of variation were higher in tempered than untempered chocolate for casein and BLG, but total and analytical CVs were comparable for peanut and egg. These findings indicate that processing has a greater effect on recovery and variability of casein and BLG than peanut and egg detection in a dark chocolate matrix.