5-Ethynyl-2'-deoxyuridine (EdU) has revolutionized DNA replication and cell cycle analyses through fast, efficient click chemistry detection. However, commercial EdU kits suffer from high costs, proprietary formulations, limited antibody multiplexing capabilities, and difficulties with larger biological specimens. Here, we present OpenEMMU (Open-source EdU Multiplexing Methodology for Understanding DNA replication dynamics), an optimized, affordable, and user-friendly click chemistry platform utilizing off-the-shelf reagents. OpenEMMU enhances efficiency, brightness, and multiplexing capabilities of EdU staining with both non-conjugated and conjugated antibodies across diverse cell types, including T cell activation and proliferation assays. We validated its effectiveness for the fluorescent imaging of nascent DNA synthesis in developing embryos and organs, including embryonic heart, forelimbs, and 3D hiPSC-derived cardiac organoids. OpenEMMU also enabled the deep-tissue 3D imaging of DNA synthesis in zebrafish larvae and under replication stress in embryos at high spatial resolution. This approach opens new avenues for understanding organismal development, cell proliferation, and DNA replication dynamics with unprecedented precision and flexibility.