Fungal allergy is a worldwide public health burden, and problems associated with a reliable allergy diagnosis are far from being solved. Especially, the lack of high-quality standardized fungal extracts contributes to the underdiagnosis of fungal allergy. Compared to the manufacturing processes of extracts from other allergen sources, the processes used to manufacture extracts from fungi show the highest variability. The reasons for the high variability are manifold as the starting material, the growth conditions, the protein extraction methods, and the storage conditions all have an influence on the presence and quantity of individual allergens. Despite the vast variety of studies that have analyzed the impact of the different production steps on the allergenicity of fungal allergen extracts, much remains unknown. This review points to the need for further research in the field of fungal allergology, for standardization and for generally accepted guidelines on the preparation of fungal allergen extracts. In particular, the standardization of fungal extracts has been and will continue to be difficult, but it will be crucial for improving allergy diagnosis and therapy.