Indigenous groups have designed and managed their ecosystems for generations, resulting in biodiversity protection while producing for their family's needs. Here we describe the agroecosystem of the Lacandon Maya, an indigenous group who live in Chiapas, Mexico. The Lacandon practice a form of swidden agriculture that conserves the surrounding rain forest ecosystem while cycling the majority of their land through five successional stages. These stages include an herbaceous stage, two shrub stages, and two forest stages. A portion of their land is kept in primary forest. This study presents the Lacandon traditional ecological knowledge (TEK) for agroforestry and quantitatively describes the plant community and the associated soil ecology of each successional stage. Also documented is the knowledge of the Lacandon regarding the immediate use of plant species and plant species useful for soil fertility enhancement. Woody plant diversity increases during the successional stages of the Lacandon system, and by the beginning of the first forest stage, the diversity is similar to that of the primary forest. In all stages, Lacandon use 60% of the available plant species for food, medicine, and raw materials. Approximately 45% of the woody plant species present in each fallow stage were thought by the Lacandon to enhance soil fertility. Total soil nitrogen and soil organic matter increased with successional stage and with time from intentional burn. Nutrient and soil nematode dynamics in shrub stages related to the presence of introduced and managed plants, indicating engineered soil enhancement by the Lacandon. The effects on biodiversity and soil ecology coupled with productivity for agricultural subsistence indicate that Lacandon TEK may offer tools for environmental conservation that would provide for a family's basic needs while maintaining a biodiverse rain forest ecosystem. Tools such as these may offer options for regional restoration and conservation efforts such as the Mesoamerican Biological Corridor in Mexico and Central America, where attainment of environmental goals must include methods to provide resources to local inhabitants.