Bimetallic heterostructures, including core-shell and Janus configurations, often offer unique electrocatalytic properties compared to monometallic nanoparticles. However, achieving precise control over both elemental composition and spatial arrangement within these structures remains a challenge. Here, an electrosynthesis method is introduced that enables the fabrication of heterostructured bimetallic nanoparticles with precise, independent control of their elemental distribution. By leveraging dual-channel scanning electrochemical cell microscopy (SECCM), the local ionic environment is dynamically modulated in situ, adjusting the deposition bias between channels to achieve selective electrodeposition. This approach allows temporal control over the solution conditions within the SECCM droplet, facilitating the synthesis of multi-layer core-shell nanoparticles with tunable thickness, number, and sequence of layers. This technique is demonstrated with Pt-Cu and Pt-Ni systems, synthesizing arrays of Cu@Pt and Pt@Cu core-shell structures, which are then screened for catalytic activity in hydrogen evolution (HER) and oxygen reduction (ORR) reactions. The high spatial resolution and on-demand control over the composition and structure make this method well-suitable for creating arrays of complex, multi-metallic heterostructures, which is expected to accelerate the discovery of advanced electrocatalytic materials, offering a platform for efficient and scalable electrocatalyst screening.