In developing countries, a common goal is to improve horticultural production systems as a strategy to increase food security and to improve the living conditions of these rural communities. However, smallholder-based agricultural systems are highly heterogeneous due to the wide range of biophysical conditions to which the crops are exposed, and the diversity in the management practices. In order to implement programs aimed at improving the productivity of these systems it is necessary to recognize its variability in quantitative terms. The main objective of this work was to describe the heterogeneity associated to smallholder production systems, using as a case study the Colombian tomato growers. Data were collected from two tomato production zones located in the Colombian Andes and under two cropping systems being the open field (OF) and the greenhouse (GH) production models. In both zones, the climate was described based on historical records, soil samples were taken to determine the natural fertility and the growers’ management practices were inquired. We also compared two instruments for data collection, surveys and detailed follow-ups. A higher heterogeneity in environmental conditions and management practices was evidenced for the OF system compared to the GH system. The fertilization strategies used by GH growers caused a significant increase in soil nutrient content, electrical conductivity and acidity. We found a higher productivity per square meter in the GH system, however the yield per plant was higher for the OF system (4.88 kg plant−1) in comparison with the GH system (2.84 kg plant−1). Results also indicated that follow-ups are an appropriate instrument to obtain accurate inventories. Knowledge empowerment arises as the key point to improve the smallholder’s productivities; in opposition to results elsewhere, where economic constraints are highlighted as the important sources of variability and low yields.