Sugar-Sweetened Beverage (SSBs) consumption has risen in early life and it is plausible that it might increase children’s risk of allergies. In this paper, we analyzed the association of SSB consumption with allergies in children’s second year of life. This study analyzed data from a São Luís BRISA prenatal cohort in the follow-up of children (n = 1144) in their second year of life. Allergy Traits were a latent variable deduced from medical diagnoses of allergic rhinitis, atopic dermatitis, and food allergies. SSBs were investigated as a percentage of daily calories based on 24 h recalls, including industrialized fruit juices, soft drinks, and ready-made chocolate milk. Other variables analyzed were socioeconomic status, age, body mass index z-score, episodes of diarrhea, and breastfeeding. Our finds were that higher consumption of daily calories from SSBs was associated with higher Allergy Trait values (SC = 0.174; p = 0.025); older age (SC = −0.181; p = 0.030) was associated with lower Allergy Trait values; and episodes of diarrhea were correlated with Allergy Traits (SC = 0.287; p = 0.015). SSB exposure was associated with Allergy Traits in children’s second year of life; thus, abstaining from these beverages may also confer additional advantages in curtailing allergic diseases during early childhood.