Well-validated methods for measuring airborne occupational allergens are essential for effective control and reduction of allergen exposures. For wheat flour allergens, specific immunoassays are available, but there is a need for optimisation and standardization of sample processing procedures. Wheat flour allergen elution and storage were studied using airborne dust samples collected in bakeries with a new parallel sampler. Forty-eight series of 9 parallel filters were subjected to extraction procedures varying in elution medium, shaking method, extraction vial, and centrifugation speed. Wheat allergens were measured with enzyme immunoassays, and the effect of various procedures evaluated by mixed regression analyses. The stability of the eluted allergens was assessed after storage for 20 days and 4 months at −20 °C, in the presence or absence of casein in the medium. Only the type of elution medium had significant effects on allergen recovery: addition of Tween-20 resulted in 3- to 100-fold increased levels, an effect that was most pronounced at low concentrations. Allergen levels in extracts were stable for at least 4 months at −20 °C, irrespective of the presence of casein in the medium. Addition of Tween-20 to the elution medium is essential for optimal extraction of wheat allergen. The recommended procedure further includes the use of conventional polystyrene tubes, simple shaking methods, and centrifugation after extraction. Wheat dust extracts in PBS-Tween can be stored frozen for at least 4 months, and addition of a stabilising protein is not required.