The system fertilization approach emerged to improve nutrient use efficiency in croplands. This new fertilization concept aims at taking advantage of nutrient cycling within an agroecosystem to obtain maximum production from each nutrient unit. To monitor this effect, methodologies such as the Normalized Difference Vegetation Index (NDVI) are promising to evaluate plant biomass and nutrient content. We evaluated the use of NDVI as a predictor of shoot biomass, P and K uptake, and yield in soybean. Treatments consisted of two production systems [integrated crop-livestock system (ICLS) and cropping system (CS)] and two periods of phosphorus (P) and potassium (K) fertilization (crop fertilization—P and K applied at soybean sowing—and system fertilization—P and K applied in the pasture establishment). NDVI was evaluated weekly from the growth stage V2 up to growth stage R8, using the Greenseeker® canopy sensor. At the growth stages V4, V6, R2, and R4, plants were sampled after NDVI evaluation for chemical analysis. Soybean yield and K uptake were similar between production systems and fertilization strategies (P > 0.05). Soybean shoot biomass and P uptake were, respectively, 25.3% and 29.7% higher in ICLS compared to CS (P < 0.05). For NDVI, an interaction between the production system and days after sowing (P < 0.05) was observed. NDVI increased to 0.95 at 96 days after sowing in CS and to 0.92 at 92 days after sowing in ICLS. A significant relationship between NDVI and shoot biomass, and P and K uptake was observed (P < 0.05). Our results show that the vegetation index NDVI can be used for estimating shoot biomass and P and K uptake in the early growth stages of soybean crops, providing farmers with a new tool for evaluating the spatial variability of soybean growth and nutrition.