Considering the need for more information about productivity increases and nutritional improvement of soils, the present study evaluated the effects of alternative fertilization on grain yield and nutritional levels of bean crops. It was a randomized block study with four treatments and five replicates. The treatments were the absence of nitrogen fertilization, fertilizer use, chicken litter, and cattle manure. Organic fertilization provided lower variations in soil water availability during flowering and grain filling and increased nutrient concentrations, especially phosphorus and potassium. Chicken litter promoted the highest means for the number of legumes, the number of legumes on branches, the number of six-grain legumes, the mass of a thousand grains, grain mass per plant, and the normalized green-red difference index. However, the two organic fertilizers had significantly higher differences from chemical and no fertilization, showing that organic fertilizer applications must occur when nutrient availability coincides with the phenological stages essential for producing these fertilizers. High yields combined with favorable rainfall conditions occurred during crop development, as high soil moisture allowed faster mineralization of essential organic fertilizer nutrients, directly affecting yield. Pearson’s linear correlation allowed a better understanding of the participation of each plant trait in productivity, and the highest grain yield occurred with organic fertilization.