Humans are the world’s greatest evolutionary force. Yet, our impacts on the evolution of Earth's microbiomes and their biogeochemical processes remain poorly understood. Notably, the overlooked potential for the intensive use of agricultural fertiliser to drive evolutionary changes in soil nutrient cycling genes warrants urgent attention. In this talk, I will present recent work where, leveraging a global dataset of >2,500 soil metagenomes, we identify increased rates of diversifying positive selection on genes involved in the reduction of nitrate (a key component of nitrogen fertilisers) in agricultural, but not natural land systems. Altered selection on genes encoding the respiratory nitrate reductase were specific to Burkholderiales, a major group of denitrifying bacteria. Protein structural analyses suggest that agriculture is driving the evolution of enzyme-substrate dynamics, likely resulting in increased rates of nitrate reduction. As Burkholderiales are dominant denitrifiers, such evolutionary consequences of agriculture on this lineage could have cascading ecological impacts. These findings indicate that anthropogenic selection can alter protein-level evolution of vital biogeochemical processes, and contribute to a deeper understanding of how human activities shape Earth's nutrient cycles, with important environmental and ecological implications.