Agriculture's most pressing challenge is raising global food production while minimising environmental degradation. Nutrient deficiencies, principally nitrogen (N), limit production requiring future increases in fertiliser use and risk to proximal non-agricultural ecosystems. We investigated combining humate with urea, globally the most widely used N-suppling fertiliser, in a four-year field study. Humate increased pasture yield by 9.8% more than urea and significantly altered soil microbial diversity and function. Humate increased N retention suggesting microbial sequestration may lower N leaching and volatilisation losses. Humic microbial bio-stimulation could feasibly increase fertiliser efficiency and development of ecologically sustainable agriculture.