This work approach the analysis of the problems caused by the incidence of allergic diseases, using an impulsive simulation model as a methodological approach, in this, the dynamics of the model is governed by two time scales, one discrete and the other continuous which represents the interaction dynamics among pollen allergens, immune system and intestinal microbiota, evidencing the variable regulation of the Thymus by sending mature T lymphocytes into the bloodstream as a pulse. Due to the complexity of the interacting systems, scientific computing is used to represents a model at the microscopic level where the particles obey a simplified dynamic. To carry out the simulations, the values of parameters used are taken from secondary sources. The scenarios described in the simulations show the behavior of helper T cells, these being an indicator of allergic reactions. The model shows that the intestinal microbiota helps Treg cells in the inhibition of the immune response, also showing that if there is a high concentration of bacteria produced by the ingestion of functional foods, it is possible to control the allergic symptoms.