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Nuts are a well-known cause of food allergy and, once this has been diagnosed, due to the likelihood of cross-sensitization to multiple tree nut allergens, their strict avoidance from the diet is advisable. In this context, we present electrochemical bioplatforms to detect traces of hazelnut and walnut in processed foods through the determination of their respective allergenic proteins Cor a 9 and Jug r 1 in a fast and sensitive assay. First, the evaluation of the single determination of both proteins was performed by building sandwich immunoconjugates on the surface of magnetic microbeads relying on specific antibodies unmodified or conjugated to horseradish peroxidase. Amperometric transduction was made upon trapping the magnetic bioconjugates on the surface of disposable carbon electrodes, using the hydroquinone/hydrogen peroxide system. The great analytical performance achieved with the individual platforms (detection limits of 0.12 and 0.56 ng mL−1 for Jug r 1 and Cor a 9, respectively), led us to the individual and dual quantification of both proteins in raw dough and baked cookies incurred with ground nuts. The developed method allowed detecting baked cookies incurred with 0.0025% ground walnut and 0.00002% ground hazelnut with results comparable to those provided by ELISA techniques. The feasibility of performing the dual determination of both allergens in a single run was demonstrated.