Over the past decades, the general trend towards shade reduction and intensification of cacao management has led to biodiversity losses. In the Peruvian Amazon, the regional government is heavily promoting crop conversion to shift from regionally marketed foods towards cacao (Theobroma cacao) and copoazu (Theobroma grandiflorum). While this shift is already visibly impacting the farming landscape and the lives of many smallholder farmers, little is known about the reasons that drive farmers to choose certain types of Theobroma species or cacao varieties over others. In this paper, we addressed how cacao farmers perceive and manage specific and varietal Theobroma diversity. We interviewed cacao farmers (n = 20) during a seed-exchange fair and adapted a version of the four-square analysis to explore which Theobromas are currently adopted by farmers and why. The native cacao variety (cacao chuncho) was the one cultivated by most farmers, followed by the more industrial clonal varieties. The source of seeds and seedlings for the most cultivated varieties was a mix of donations by public institutions (for clonal varieties) and informal exchange among farmers (mainly for native and criollo varieties, and species i.e. macambo (Theobroma bicolor) and cacauillo (Theobroma speciosum)). The cacao varieties incentivized by public institutions were the least desired for future investment. The motivations for farmers to plant Theobromas was mainly based on the perceived current and potential market, but their desire to invest in a given species or variety was also based on pest resistance, traditional use, farm diversification and taste. Copoazu and CCN cacao varieties are produced by many households in large areas, while macambo, cacauillo and the cacao varieties TSH and porcelana are produced by few households in small areas. Our study suggests that agroforestry systems that include alternative Theobroma species are multi-strata and more diverse than cacao-based systems. It highlights the risks of agrobiodiversity loss associated with the promotion of industrial cacao varieties, and the importance of seed and seedling access for the development of diverse farming systems. We recommend the expansion of local seed-sharing networks and the extension of public cacao-donation campaigns to neglected and underutilized Theobromas with socio-economic and environmental benefits, in order to make the local farming systems more diverse and resilient.