Allergen-specific immunotherapy is emerging as a viable avenue for treatment of food allergy. Clinical trials currently investigate raw or slightly processed foods as therapeutic agents, as trials using food-grade agents can be performed without the strict regulations to which conventional drugs are subjected. However, this limits the ability of standardization and may affect clinical trial outcomes and reproducibility. Herein, we provide an overview of methods used in the production of immunotherapeutic agents for the treatment of food allergy, including processed foods, allergen extracts, recombinant allergens, and synthetic peptides, as well as the physical and chemical processes for the reduction of protein allergenicity. Commercial interests currently favor producing standardized drug-grade allergen extracts for therapeutic use, and clinical trials are ongoing. In the near future recombinant production could replace purification strategies since it allows manufacturing pure, native allergens or sequence-modified allergens with reduced allergenicity. A recurring issue within the field is the inadequate reporting on production procedures, quality control, product physicochemical characteristics, allergenicity and immunological properties. This information is of vital importance in assessing therapeutic standardization and clinical safety profile, which are central parameters for development of future therapeutic agents.