The methods of sowing and the specific conditions of the seeds used have a significant impact on the complex process of plant growth. The choice of seed location not only reflects the genetic and physiological characteristics of the plant but also helps to make it healthier. This, in turn, leads to improved growth and higher yields in various agricultural environments. In this study, an experimental design was implemented to analyze different methods of planting cacao seeds to determine which method is most effective in minimizing root and hypocotyl malformations. For the seeding process, it was ensured that all samples were from the same source. Two types of substrates and three different levels of seed placement were selected to serve as the basis for cultivation in soil contained in polyethylene bags. The experimental design was randomized with two factors and three levels, resulting in a total of 18 samples. The results were analyzed using the Design of Experiments (DOE) methodology in Minitab® software, along with photographic documentation of seed growth after 15 days. The analysis revealed that the seeds sown in the vertical position had fewer malformations. Specifically, 83% of the total samples fell into this category, which is consistent with a normal distribution. It can therefore be concluded that vertical seed positioning is the most effective planting method for promoting healthy growth and minimizing malformations.