Fertilization is considered as one of the main sources of environmental pollution caused by agriculture. When high fertilizer rates are applied, nutrient losses take place which pollute agricultural ecosystems. Defense strategies were developed in order to minimize the environmental burden caused by agricultural pollution. One of these strategies is based on the usage of biofertilizers – microorganisms isolated from soil that can stimulate plant growth. In this context, effects of a Bacillus pumilus strain isolated from soybean rhizosphere on plant growth, nodulation and seed protein yield were investigated. Two factors (A x B) experiments were conducted using a “split plots design”. The soybean plants have been grown in ecological conditions, without organic fertilizers and pesticides. Our results suggest that the tested rhizobacterial strain significantly increased the plant’s height (p<0.0001), number of leaves (p<0.0003), foliar area (p<0.0002), nodulation (p<0.0002) and bean protein content (p<0.05), compared to the non-treated control. We concluded that Bacillus pumilus Rs3 promoted plant growth and increased seed protein yield. Our rhizobacterial strain could be an eco-friendly alternative for reducing soil pollution caused by fertilizers usage.