Seed microbiolization is an alternative to chemical pesticides for seed treatment in organic agriculture. Thus, this study aimed at evaluating the initial growth and control of fungi associated with organic cotton seeds, through seed microbiolization with Trichoderma sp. and Saccharomyces cerevisiae. Certified cotton seeds (cultivar Aroeira), whose linter was removed with sulfuric acid, were analyzed in a completely randomized design in a 5 x 2 + 1 factorial scheme, corresponding to five concentrations (0, 0.5, 1.0, 1.5, and 2.0), two biocontrol agents (Trichoderma sp. and S. cerevisiae), and an additional treatment composed of a fungicide (Captan®). Seed health, germination, and emergence tests were conducted to confirm the hypotheses. The microbiolization of seeds is efficient in reducing both incidence and initial growth of fungi in organic cotton cv. Aroeira. The appraised biocontrol agents proved to be superior to the chemical treatment regarding the initial seedling growth. Trichoderma sp. is the most effective agent and provides a high initial seedling growth and a significant reduction in fungal incidence.