Changing climatic conditions impose a challenge both to biodiversity and food security. The effects of climate change affect different aspects of the plant or crop, such as morphological and phenological aspects, as well as yield. The effects of greenhouse conditions might be comparable in some cases to a permanent extreme disturbance in climate and weather, thus, contributing to our knowledge on climate change impacts on plant species. We have investigated the differences for 23 traits in two cultivar groups of an Andean traditional crop, Solanum betaceum, under two different environmental conditions that correspond to the traditional practices in the open field and three cultural managements under greenhouse conditions (no fertilization or control, organic, and mineral). We found that traditional practices in the open field are the less productive. Moreover, in warmer and drier conditions the treatment with organic fertilization was the most productive. Greenhouse conditions, however, delay production. We further identified traits that differentiate both cultivar groups and traits that are linked to either the new climate conditions or the fertilization treatments. Fruit characteristics were quite homogeneous between the two cultivar groups. Overall, our results provide insight on the consequences that climate change effects might exert on crops such as tree tomato, reveal that greenhouses can be a robust alternative for tree tomato production, and highlight the need to understand how different managements are linked to different solutions to fulfil the farmers’ demands.