This paper’s working hypothesis is that the indigenous farming practices of Timorese farmers are those most suitable and adaptable with regard to these farmers’ circumstances. Intensive farming and the acceleration of land conversion in Java lead to a reduction in favorable cropland and the degradation of soil biology. To meet the demand for food production, unfavorable areas outside Java, including marginal semi-arid areas on Timor Island, East Nusa Tenggara province, have become an important option. Unfortunately, the national crop production policy has paid less attention to the specific biophysical characteristics of the region and how local people have adapted to the diverse marginal environment. We review the literature in the areas of soil nutrition retention and soil biology, vegetation/crop diversity, and farming practices/management, including local wisdom on soil management. This paper highlights that the values of the chemical parameters of the soils in question are varied, but generally range from low to high. The existence of beneficial micro-organisms is important both for improving soil fertility and due to their association with local vegetation/crops. Traditional farming practices, such as the local agroforestry of Mamar, have effectively preserved the existence of micro-organisms that promote conservation practices, crop/vegetation diversity, and sustainable agriculture. We recommend that the expansion of croplands and crop production into marginal semi-arid areas needs to be considered and adapted while taking into consideration sustainability and environmentally sound traditional practices.