Reliable detection and quantification of allergens are essential in order to protect allergic consumers and to comply with labeling regulations. In recent years various allergen-detection methods have been published, and test kits have become commercially available. Due to the nature of the analytes (usually allergenic proteins, specific marker proteins, or specific DNA markers) and their susceptibility to various processing effects, reliability and comparability of results have posed a great challenge. Often processing and matrix effects hamper the extraction efficiency and the quantitative analysis of allergens or markers in food products. Both reference methods and reference materials are urgently needed in the field of allergen testing. The EU-funded Network of Excellence, MoniQA—Monitoring and Quality Assurance in the Total food Supply Chain (www.moniqa.org)—is working toward the harmonization of monitoring and control strategies for food quality and safety assessment and thus focuses on performance criteria for methods used to analyze foods and food products for safety and quality. MoniQA established various analyte-specific working groups: Microbiological Contaminants, Mycotoxins and Phycotoxins, Chemical Contaminants, Food Allergens, Food Additives and Processing Toxicants, Food Authenticity, and Emerging Issues. MoniQA’s Food Allergen Working Group (WG) is compiling information about the most important food allergens, identifying gaps, prioritizing requirements, and developing harmonization guidelines in collaboration with all stakeholder groups, which include industry, food authorities, consumers, and laboratories. The WG works on (1) harmonized validation protocols and certification criteria for allergen testing, (2) status recognition of allergen methods which underwent a validation trial, (3) reference/testing materials, (4) international ring trials for full validation of new reference/testing materials and analytical methods, and (5) the development of a reference method by supporting research toward the improved use of mass spectrometry in food allergen testing. Additionally training for research and industry in the areas of analytical method development, method validation and verification, allergen management, and risk communication and a database on available analytical methods, validation level, and legislation linked with the RASFF—EU’s Rapid Alert System for Food and Feed are provided.