The construction industry is responsible for a considerable share of the carbon emissions annually. Despite the wide body of literature addressing the embodied carbon of superstructures, limited attention is given to the embodied carbon of substructures. This research introduces an optimization algorithm to minimize the embodied carbon of deep foundations. The algorithm is used to optimize and then compare the embodied carbon of concrete, timber, and steel piles at different pile capacities. Results show that for clay soils and low pile capacities, timber piles are the least emitting compared to other materials, while steel piles are the highest emitting. The algorithm is then applied to a case study in London clay and demonstrated embodied carbon savings of up to 76% compared to current pile designs showing a high potential to reduce the embodied carbon and achieve the net-zero future goal in the construction industry.