The controlled transformation of cacao seeds by adjusting the pH by using organic acid solutions is valuable for obtaining high-quality products with enhanced characteristics. This study aimed to evaluate the impact of organic acids on the microstructure of cacao seeds under specific operating conditions that emphasize cacao quality-related characteristics. Confocal laser scanning microscopy and scanning electron microscopy were employed to describe the seed microstructure and characterize the presence of autofluorescent cellular components through image analysis, as well as to obtain the fractal dimension and texture parameters of the seeds. The results revealed significant differences in the microstructural characteristics of the seeds among the different treatments applied. Acetic acid treatment increased membrane permeability, causing a reduction in cell volume. In contrast, lactic acid treatment resulted in the formation of smaller vacuolar inclusions of anthocyanins within the cotyledon, accompanied by a higher presence of phenolic compound aggregates. Conversely, the controlled transformation using citric acid resulted in minimal cell damage to the seed structures, resulting in a more uniform and homogeneous texture. These findings provide valuable insights into the microstructural changes induced by organic acids and their potential to improve cacao processing methods, focusing on enhancing quality-related aspects vital for developing cacao products.