Allergy to novel food proteins, due to diverse ingredients and innovative food processing technologies employed to achieve desired functional properties, is a major safety concern. Current allergy testing methods (ELISA and mass spectrometry) depend on high-quality protein extracts, meaning existing methods are often tailored to specific matrices. Therefore, a more efficient and general protein extraction method is desirable for comprehensive allergy risk assessment. Here, we developed a highly efficient and reproducible protein extraction method which achieved at least 80 % efficiency across several food matrices. Proteomics analysis of a plant-based meat using our optimized extraction method showed that higher extraction efficiency improved reproducibility of identified proteins. Moreover, higher protein extraction efficiency resulted in increased abundances of individual allergenic proteins. This underscores the relevance of our method for more accurate measurements of allergenic protein concentrations in allergy risk assessments.