Microfluidics enables precise control of fluid movement within microchannels, facilitating the generation of microdroplets at high frequencies. This technology provides a unique platform for conducting biological and chemical experiments, enhancing throughput and sensitivity, particularly in single-cell analysis. The microdroplet environment enhances interactions between cells and gene delivery materials, resulting in greater contact area, higher reagent concentration, and improved diffusion for both eukaryotic and prokaryotic cells. This review discusses the advantages and limitations of transfection and transformation within microdroplet technologies, highlighting their potential to improve gene editing efficiency while addressing challenges related to delivery mechanisms and cellular uptake rates. The integration of microdroplet technology with advanced gene editing tools, such as CRISPR/Cas9, promises to streamline processes and improve outcomes in various applications, including therapeutic interventions, vaccine development, regenerative medicine, and personalized medicine. These advancements could lead to more precise targeting of genetic modifications, resulting in tailored therapies that better meet individual patient needs. Overall, the integration of gene delivery in microdroplets represents a significant leap in biotechnology, enhancing the efficacy of gene delivery systems and opening new avenues for research and development in precision medicine.