Different cocoa populations have demonstrated a protective role in a rat model of allergic asthma by attenuating the immunoglobulin (Ig) E synthesis and partially protecting against anaphylactic response. The aim of this study was to ascertain the effect of diets containing two native Peruvian cocoa populations (“Amazonas Peru” or APC, and “Criollo de Montaña” or CMC) and an ordinary cocoa (OC) on the bronchial compartment and the systemic and mucosal immune system in the same rat model of allergic asthma. Among other variables, cells and IgA content in the bronchoalveolar lavage fluid (BALF) and serum anti-allergen antibody response were analyzed. The three cocoa populations prevented the increase of the serum specific IgG1 (T helper 2 isotype). The three cocoa diets decreased asthma-induced granulocyte increase in the BALF, which was mainly due to the reduction in the proportion of eosinophils. Moreover, both the OC and CMC diets were able to prevent the leukocyte infiltration caused by asthma induction in both the trachea and nasal cavity and decreased the IgA in both fecal and BALF samples. Overall, these results highlight the potential of different cocoa populations in the prevention of allergic asthma.