The development of green recycling technology for precious metals such as Ag and Pd from secondary resources can prevent environmental pollution caused by improper disposal, and it can alleviate resource shortage and promote sustainable development. Ag and Pd often coexist in some solid waste. This study proposed the extraction of Ag and Pd stepwise from leachate through the green technology of potential-controlled electrodeposition, and the reduction potential difference of Ag and Pd in solution was increased based on EDTA (ethylenediaminetetraacetic acid) complexation. The electrochemical behavior of Ag+ and Pd2+ in solution was investigated. It was determined that the electrodeposition separation of Ag+ and Pd2+ can be achieved with a pH of 9 and an EDTA molar ratio of 1:1.5 in the solution. With sequential electrodeposition at 0 V and −0.7 V, 99.3% of Ag and 96.15% of Pd were recovered, respectively, and their purity was achieved 100%. Pd electrodeposition conformed to three-dimensional instantaneous nucleation and growth mechanism analyzed with the Scharifker–Hills model. Compared with the EDTA-free environment, the diffusion coefficient of ions reduced, and the activation energy of Ag and Pd reduction reaction increased in the EDTA environment. This study provides an environmentally friendly and efficient method for precious metal recovery from secondary resources.