Due to the worldwide prevalence of food allergies, many countries have mandated allergen labeling. The presence of undeclared allergens can occur from cross-contamination during food processing, which is often mitigated by including “may contain” product labels. Although "vegan" or "plant-based" products claims are not regulated, traces of egg and milk have been reported in these foods, leading to unexpected allergic reactions. ELISA is commonly used for food allergen quantitation, but this technique suffers from cross-reactivity, variability between supplier kits and is typically limited to only single-allergen detection. In contrast, LC-MS/MS is capable of multi-allergen detection with high sensitivity and selectivity required for food matrices. Here, a sample preparation and LC-MS/MS method achieved limits of quantitation (LOQs) in the range of 0.1–10 mg allergen/kg food for milk and egg allergen peptides. These LOQs enabled detection at levels below the recommended sensitivity required for complying with the VITAL program and AOAC SMPR. When quantified by matrix-matched calibration, matrix spikes at the LOQ and at 10 and 50 mg allergen/kg food demonstrated apparent recoveries of 75–128%. Absolute recoveries ranged from 25–86% in cookie and cheese, while <20% recoveries were obtained in cake mix. These lower recoveries are consistent with the literature and provide realistic insights into how incurred allergens are lost during sample preparation. Method application to commercial foods accurately reflected the presence of milk and egg allergens expected from most products, but several samples exhibited positive detection despite the undeclared allergens in the ingredients list.