Agricultural production systems demand techniques that allow reducing uncertainty in decision-making. A factor that adds uncertainty in agricultural systems is altitude since it influences the nutrient uptake by plants. This work aimed to evaluate the influence of two altitudinal gradients (2569 and 1487 m.a.s.l.) and two fertilizers: an organo-mineral fertilizer (composted poultry manure mixed with inorganic fertilizer) and mineral fertilizer (control) on the nutrient uptake and biomass production in commercial stevia crops. The effect of altitude and fertilizers was evaluated after 60 days, under greenhouse conditions, assessing macro and micronutrient levels in the plant leaves (nitrogen, phosphorus, potassium, calcium, magnesium, sulfur, manganese, zinc, iron, and boron) and biomass production. The results of this work showed the effect of altitude (2569 m.a.s.l.) and organo-mineral fertilization on crop productivity and yield. The application of the organo-mineral fertilizer decreased the differences of nutrient uptake between the altitudinal gradients and provided both better nutrient uptake levels, mainly of N (79%), Ca (115%), and Mg (162%), and increased biomass production (49%), than mineral fertilization at both experimental sites. Likewise, the organo-mineral fertilizer enhanced the soils’ cation exchange capacity, increased nutrient availability, and minimizing the risks of contamination by nutrient leaching. An important conclusion of this work is that stevia plants grown at different altitudes differ in nutrient uptake (mostly nitrogen 79%); therefore, fertilizer dosing must be adjusted to crop altitude, especially for mineral fertilizers. Thus, fertilizer design should consider not only the plant nutrition requirements but also its environmental conditions.